Starting phenix.real_space_refine
on Wed Mar  4 15:39:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x5a_22047/03_2026/6x5a_22047.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x5a_22047/03_2026/6x5a_22047.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x5a_22047/03_2026/6x5a_22047.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x5a_22047/03_2026/6x5a_22047.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x5a_22047/03_2026/6x5a_22047.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x5a_22047/03_2026/6x5a_22047.cif"
  }
  resolution = 4.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     288      5.49       5
     S      23      5.16       5
     C    8541      2.51       5
     N    2764      2.21       5
     O    3346      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14963
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 809
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 637
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 828
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 809
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 645
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2954
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2985
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 2993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2993
          Classifications: {'peptide': 362}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 345}
    Chain: "K"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.14, per 1000 atoms: 0.21
  Number of scatterers: 14963
  At special positions: 0
  Unit cell: (129.47, 116.63, 133.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      23     16.00
     P     288     15.00
     O    3346      8.00
     N    2764      7.00
     C    8541      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: 1.02
  Conformation dependent library (CDL) restraints added in 464.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 601 "
        pdb="ZN    ZN K 601 " - pdb=" NE2 HIS K 378 "


  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 13 sheets defined
      62.9% alpha, 8.2% beta
      142 base pairs and 253 stacking pairs defined.
    Time for finding SS restraints: 1.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.687A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.715A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.524A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.254A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.836A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.878A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.592A  pdb=" N   MET D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.858A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.687A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.715A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.524A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    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: 4.048A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.599A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
      removed outlier: 3.628A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.845A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.502A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 57 through 84
      removed outlier: 3.629A  pdb=" N   ASN H  63 " --> pdb=" O   MET H  59 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 3.575A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 147 through 183
      removed outlier: 3.906A  pdb=" N   GLU K 166 " --> pdb=" O   LYS K 162 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 248 through 250
      No H-bonds generated for 'chain 'K' and resid 248 through 250'
    Processing helix  chain 'K' and resid 258 through 276
    Processing helix  chain 'K' and resid 319 through 323
    Processing helix  chain 'K' and resid 333 through 342
      removed outlier: 3.666A  pdb=" N   ARG K 337 " --> pdb=" O   GLY K 333 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 367 through 377
    Processing helix  chain 'K' and resid 393 through 412
    Processing helix  chain 'K' and resid 419 through 434
      removed outlier: 4.352A  pdb=" N   VAL K 423 " --> pdb=" O   CYS K 419 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 436 through 440
    Processing helix  chain 'K' and resid 441 through 443
      No H-bonds generated for 'chain 'K' and resid 441 through 443'
    Processing helix  chain 'K' and resid 444 through 462
      removed outlier: 3.510A  pdb=" N   THR K 462 " --> pdb=" O   GLU K 458 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 482 through 499
    Processing helix  chain 'K' and resid 500 through 506
      removed outlier: 6.087A  pdb=" N   ILE K 503 " --> pdb=" O   GLY K 500 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS K 506 " --> pdb=" O   ILE K 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.886A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.451A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.255A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.295A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
      removed outlier: 3.527A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'K' and resid 192 through 195
      removed outlier: 3.978A  pdb=" N   MET K 215 " --> pdb=" O   LEU K 195 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   PHE K 212 " --> pdb=" O   ASP K 307 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ILE K 309 " --> pdb=" O   PHE K 212 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   VAL K 214 " --> pdb=" O   ILE K 309 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ALA K 311 " --> pdb=" O   VAL K 214 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   PHE K 216 " --> pdb=" O   ALA K 311 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   GLU K 313 " --> pdb=" O   PHE K 216 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LEU K 218 " --> pdb=" O   GLU K 313 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU K 310 " --> pdb=" O   PRO K 349 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 192 through 195
      removed outlier: 3.978A  pdb=" N   MET K 215 " --> pdb=" O   LEU K 195 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   PHE K 212 " --> pdb=" O   ASP K 307 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ILE K 309 " --> pdb=" O   PHE K 212 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   VAL K 214 " --> pdb=" O   ILE K 309 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ALA K 311 " --> pdb=" O   VAL K 214 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   PHE K 216 " --> pdb=" O   ALA K 311 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   GLU K 313 " --> pdb=" O   PHE K 216 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LEU K 218 " --> pdb=" O   GLU K 313 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL K 294 " --> pdb=" O   ILE K 308 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   THR K 295 " --> pdb=" O   GLU K 285 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 252 through 253

    529 hydrogen bonds defined for protein.
    1545 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      363 hydrogen bonds
      722 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      253 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3189
        1.33 -     1.45: 4638
        1.45 -     1.57: 7387
        1.57 -     1.69: 577
        1.69 -     1.81: 38
  Bond restraints: 15829
  Sorted by residual:
  bond pdb=" C3'  DT J  57 "
       pdb=" O3'  DT J  57 "
    ideal  model  delta    sigma   weight residual
    1.422  1.361  0.061 3.00e-02 1.11e+03 4.20e+00
  bond pdb=" CB  ILE K 493 "
       pdb=" CG2 ILE K 493 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.13e+00
  bond pdb=" CG  ARG K 177 "
       pdb=" CD  ARG K 177 "
    ideal  model  delta    sigma   weight residual
    1.520  1.574 -0.054 3.00e-02 1.11e+03 3.22e+00
  bond pdb=" C   LEU D 101 "
       pdb=" N   LEU D 102 "
    ideal  model  delta    sigma   weight residual
    1.340  1.237  0.103 5.87e-02 2.90e+02 3.09e+00
  bond pdb=" C   LEU K 326 "
       pdb=" O   LEU K 326 "
    ideal  model  delta    sigma   weight residual
    1.233  1.225  0.008 4.80e-03 4.34e+04 3.01e+00
  ... (remaining 15824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 22077
        2.42 -     4.84: 454
        4.84 -     7.25: 48
        7.25 -     9.67: 10
        9.67 -    12.09: 2
  Bond angle restraints: 22591
  Sorted by residual:
  angle pdb=" CA  ARG K 299 "
        pdb=" CB  ARG K 299 "
        pdb=" CG  ARG K 299 "
      ideal   model   delta    sigma   weight residual
     114.10  123.36   -9.26 2.00e+00 2.50e-01 2.14e+01
  angle pdb=" CA  LYS K 409 "
        pdb=" CB  LYS K 409 "
        pdb=" CG  LYS K 409 "
      ideal   model   delta    sigma   weight residual
     114.10  122.79   -8.69 2.00e+00 2.50e-01 1.89e+01
  angle pdb=" CA  LYS K 391 "
        pdb=" CB  LYS K 391 "
        pdb=" CG  LYS K 391 "
      ideal   model   delta    sigma   weight residual
     114.10  122.02   -7.92 2.00e+00 2.50e-01 1.57e+01
  angle pdb=" N   LYS K 160 "
        pdb=" CA  LYS K 160 "
        pdb=" C   LYS K 160 "
      ideal   model   delta    sigma   weight residual
     111.02  106.37    4.65 1.22e+00 6.72e-01 1.45e+01
  angle pdb=" CB  ARG K 244 "
        pdb=" CG  ARG K 244 "
        pdb=" CD  ARG K 244 "
      ideal   model   delta    sigma   weight residual
     111.30  119.99   -8.69 2.30e+00 1.89e-01 1.43e+01
  ... (remaining 22586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.36: 7272
       35.36 -    70.72: 1526
       70.72 -   106.08: 23
      106.08 -   141.43: 1
      141.43 -   176.79: 2
  Dihedral angle restraints: 8824
    sinusoidal: 5557
      harmonic: 3267
  Sorted by residual:
  dihedral pdb=" CA  LYS K 353 "
           pdb=" C   LYS K 353 "
           pdb=" N   ASP K 354 "
           pdb=" CA  ASP K 354 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.45  -42.55     0      5.00e+00 4.00e-02 7.24e+01
  dihedral pdb=" CA  LYS A  37 "
           pdb=" C   LYS A  37 "
           pdb=" N   PRO A  38 "
           pdb=" CA  PRO A  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.69  -26.31     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  LYS E  37 "
           pdb=" C   LYS E  37 "
           pdb=" N   PRO E  38 "
           pdb=" CA  PRO E  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.70  -26.30     0      5.00e+00 4.00e-02 2.77e+01
  ... (remaining 8821 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1715
       0.045 -    0.090: 671
       0.090 -    0.135: 127
       0.135 -    0.180: 22
       0.180 -    0.226: 5
  Chirality restraints: 2540
  Sorted by residual:
  chirality pdb=" CG  LEU K 415 "
            pdb=" CB  LEU K 415 "
            pdb=" CD1 LEU K 415 "
            pdb=" CD2 LEU K 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE B  50 "
            pdb=" CA  ILE B  50 "
            pdb=" CG1 ILE B  50 "
            pdb=" CG2 ILE B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" C1'  DC I  25 "
            pdb=" O4'  DC I  25 "
            pdb=" C2'  DC I  25 "
            pdb=" N1   DC I  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.25    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 2537 not shown)

  Planarity restraints: 1858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU E  59 "   -0.020 2.00e-02 2.50e+03   4.10e-02 1.68e+01
        pdb=" CD  GLU E  59 "    0.071 2.00e-02 2.50e+03
        pdb=" OE1 GLU E  59 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE2 GLU E  59 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  59 "   -0.020 2.00e-02 2.50e+03   4.08e-02 1.67e+01
        pdb=" CD  GLU A  59 "    0.071 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  59 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  59 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO F  32 "    0.019 2.00e-02 2.50e+03   3.71e-02 1.37e+01
        pdb=" C   PRO F  32 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   PRO F  32 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ALA F  33 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1855 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 535
        2.67 -     3.22: 13722
        3.22 -     3.78: 27799
        3.78 -     4.34: 35201
        4.34 -     4.90: 51239
  Nonbonded interactions: 128496
  Sorted by model distance:
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" N   LYS B  79 "
            pdb=" OP1  DA J 101 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" NH2 ARG E  42 "
            pdb=" OP1  DG J  68 "
     model   vdw
     2.154 3.120
  nonbonded pdb=" NH2 ARG A  69 "
            pdb=" OP2  DA J  90 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O2   DC I  94 "
            pdb=" N2   DG J  52 "
     model   vdw
     2.174 2.496
  ... (remaining 128491 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 10 through 116)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 31 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.350
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.263  15830  Z= 0.334
  Angle     :  0.893  12.088  22591  Z= 0.524
  Chirality :  0.048   0.226   2540
  Planarity :  0.007   0.057   1858
  Dihedral  : 26.988 176.793   6712
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 17.78
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.15 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.27 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.22), residues: 1105
  helix: -0.44 (0.18), residues: 676
  sheet: -1.46 (0.63), residues: 52
  loop : -2.76 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG K 299 
 TYR   0.021   0.002   TYR B  72 
 PHE   0.029   0.002   PHE K 476 
 TRP   0.026   0.003   TRP K 440 
 HIS   0.010   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00722 (15829)
  covalent geometry    : angle       0.89302 (22591)
  hydrogen bonds       : bond        0.13469 (  889)
  hydrogen bonds       : angle       4.78508 ( 2267)
  metal coordination   : bond        0.26343 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 260
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8753 (mt-10)
REVERT: A   54 TYR cc_start: 0.8712 (m-80) cc_final: 0.8177 (m-80)
REVERT: A   55 GLN cc_start: 0.8998 (mt0) cc_final: 0.8104 (tt0)
REVERT: A   56 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8550 (mmmt)
REVERT: A   67 PHE cc_start: 0.8178 (t80) cc_final: 0.7798 (t80)
REVERT: A   73 GLU cc_start: 0.8897 (pt0) cc_final: 0.8488 (pt0)
REVERT: A   85 GLN cc_start: 0.9574 (mt0) cc_final: 0.8944 (mm110)
REVERT: A  107 THR cc_start: 0.9260 (p) cc_final: 0.9050 (p)
REVERT: B   72 TYR cc_start: 0.9327 (m-80) cc_final: 0.9048 (m-10)
REVERT: B   88 TYR cc_start: 0.9301 (m-10) cc_final: 0.8408 (m-10)
REVERT: C   38 ASN cc_start: 0.8638 (m-40) cc_final: 0.8250 (t0)
REVERT: D   59 MET cc_start: 0.8549 (tpp) cc_final: 0.8133 (tmm)
REVERT: D   83 TYR cc_start: 0.8520 (m-10) cc_final: 0.7344 (m-10)
REVERT: E   46 VAL cc_start: 0.8073 (t) cc_final: 0.7364 (t)
REVERT: E   50 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8611 (mt-10)
REVERT: E   85 GLN cc_start: 0.8770 (mt0) cc_final: 0.8503 (mt0)
REVERT: E  106 ASP cc_start: 0.9206 (m-30) cc_final: 0.8904 (m-30)
REVERT: F   37 LEU cc_start: 0.9393 (mt) cc_final: 0.9181 (tt)
REVERT: F   58 LEU cc_start: 0.9354 (tp) cc_final: 0.9126 (tt)
REVERT: F   74 GLU cc_start: 0.8841 (pt0) cc_final: 0.8620 (pt0)
REVERT: G   38 ASN cc_start: 0.8907 (m110) cc_final: 0.8349 (m110)
REVERT: G   90 ASP cc_start: 0.8807 (t70) cc_final: 0.8581 (t0)
REVERT: G   99 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8613 (mmmm)
REVERT: H  113 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9099 (mm-30)
REVERT: K  215 MET cc_start: 0.7058 (mtt) cc_final: 0.6730 (mpp)
REVERT: K  430 MET cc_start: -0.0038 (tpt) cc_final: -0.0257 (ttt)
REVERT: K  467 HIS cc_start: 0.7160 (t-90) cc_final: 0.6875 (t-90)
  outliers start: 16
  outliers final: 4
  residues processed: 272
  average time/residue: 0.1367
  time to fit residues: 51.6748
Evaluate side-chains
  134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   overall best weight:    6.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  24 GLN
C  31 HIS
D  63 ASN
D  95 GLN
E  68 GLN
F  75 HIS
F  93 GLN
G  31 HIS
G  84 GLN
G  89 ASN
H  95 GLN
K 183 GLN
** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.052931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.032914 restraints weight = 141387.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.033470 restraints weight = 82609.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.033733 restraints weight = 59885.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 72)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.034058 restraints weight = 48381.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.034185 restraints weight = 45284.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  15830  Z= 0.292
  Angle     :  0.742   8.547  22591  Z= 0.421
  Chirality :  0.041   0.164   2540
  Planarity :  0.006   0.051   1858
  Dihedral  : 30.284 175.089   4405
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.81 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.24), residues: 1105
  helix:  0.93 (0.19), residues: 690
  sheet: -1.26 (0.72), residues: 50
  loop : -2.27 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG K 161 
 TYR   0.022   0.002   TYR K 373 
 PHE   0.016   0.002   PHE K 476 
 TRP   0.011   0.002   TRP K 431 
 HIS   0.010   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 (15829)
  covalent geometry    : angle       0.74225 (22591)
  hydrogen bonds       : bond        0.07199 (  889)
  hydrogen bonds       : angle       3.93917 ( 2267)
  metal coordination   : bond        0.00116 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8778 (mp0)
REVERT: A   54 TYR cc_start: 0.9032 (m-80) cc_final: 0.8422 (m-80)
REVERT: A   56 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8660 (mmmt)
REVERT: A   85 GLN cc_start: 0.9646 (mt0) cc_final: 0.9282 (mm-40)
REVERT: A   97 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: B   68 ASP cc_start: 0.9302 (m-30) cc_final: 0.9089 (m-30)
REVERT: B   84 MET cc_start: 0.8596 (mmp) cc_final: 0.7683 (tpp)
REVERT: B   88 TYR cc_start: 0.9180 (m-10) cc_final: 0.8319 (m-80)
REVERT: E  100 LEU cc_start: 0.9562 (tp) cc_final: 0.9263 (tp)
REVERT: E  107 THR cc_start: 0.9493 (p) cc_final: 0.9194 (p)
REVERT: E  120 MET cc_start: 0.8900 (mmp) cc_final: 0.8485 (mmm)
REVERT: F   37 LEU cc_start: 0.9576 (mt) cc_final: 0.9354 (tt)
REVERT: G   38 ASN cc_start: 0.8996 (m110) cc_final: 0.8491 (p0)
REVERT: G   99 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8573 (mmmt)
REVERT: H   71 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9116 (tm-30)
REVERT: K  201 TYR cc_start: 0.3801 (m-10) cc_final: 0.3102 (m-10)
REVERT: K  215 MET cc_start: 0.6881 (mtt) cc_final: 0.6588 (mpp)
REVERT: K  326 LEU cc_start: 0.4581 (tp) cc_final: 0.3427 (tp)
REVERT: K  365 LEU cc_start: 0.8055 (mp) cc_final: 0.7751 (mp)
REVERT: K  432 THR cc_start: 0.1972 (t) cc_final: 0.1647 (p)
REVERT: K  467 HIS cc_start: 0.7237 (t-90) cc_final: 0.6937 (t-90)
REVERT: K  468 TYR cc_start: 0.5508 (t80) cc_final: 0.4646 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1311
  time to fit residues: 30.0621
Evaluate side-chains
  98 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 102 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 113 HIS
D  47 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E 113 HIS
F  25 ASN
** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 478 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.052951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.033224 restraints weight = 141921.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.033746 restraints weight = 80449.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.034092 restraints weight = 57573.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.034327 restraints weight = 47946.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.034382 restraints weight = 43572.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  15830  Z= 0.211
  Angle     :  0.640  10.132  22591  Z= 0.367
  Chirality :  0.038   0.150   2540
  Planarity :  0.005   0.052   1858
  Dihedral  : 30.196 173.542   4405
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.36 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.26), residues: 1105
  helix:  1.47 (0.20), residues: 692
  sheet: -1.16 (0.74), residues: 50
  loop : -1.96 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 177 
 TYR   0.016   0.002   TYR F  51 
 PHE   0.022   0.002   PHE H  65 
 TRP   0.014   0.002   TRP K 331 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (15829)
  covalent geometry    : angle       0.63972 (22591)
  hydrogen bonds       : bond        0.05377 (  889)
  hydrogen bonds       : angle       3.64869 ( 2267)
  metal coordination   : bond        0.00079 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9015 (mp0)
REVERT: A   54 TYR cc_start: 0.9052 (m-80) cc_final: 0.8417 (m-80)
REVERT: A   56 LYS cc_start: 0.8986 (ttmt) cc_final: 0.8729 (mmmt)
REVERT: B   61 PHE cc_start: 0.9430 (t80) cc_final: 0.9204 (t80)
REVERT: D  102 LEU cc_start: 0.9646 (mm) cc_final: 0.9439 (mm)
REVERT: E  100 LEU cc_start: 0.9536 (tp) cc_final: 0.9321 (tp)
REVERT: E  106 ASP cc_start: 0.9206 (m-30) cc_final: 0.8995 (m-30)
REVERT: F   37 LEU cc_start: 0.9541 (mt) cc_final: 0.9333 (tt)
REVERT: G   38 ASN cc_start: 0.8947 (m110) cc_final: 0.8407 (p0)
REVERT: G   51 LEU cc_start: 0.9633 (tp) cc_final: 0.9230 (pp)
REVERT: G   99 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8471 (mmmt)
REVERT: H   71 GLU cc_start: 0.9436 (tm-30) cc_final: 0.9056 (tm-30)
REVERT: H   93 GLU cc_start: 0.9253 (mp0) cc_final: 0.8872 (mp0)
REVERT: H  100 LEU cc_start: 0.9483 (tp) cc_final: 0.9282 (tp)
REVERT: H  108 LYS cc_start: 0.9400 (mmtm) cc_final: 0.9097 (pttt)
REVERT: K  215 MET cc_start: 0.6937 (mtt) cc_final: 0.6569 (mpp)
REVERT: K  326 LEU cc_start: 0.4981 (tp) cc_final: 0.4418 (tp)
REVERT: K  467 HIS cc_start: 0.7061 (t-90) cc_final: 0.6746 (t-90)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1235
  time to fit residues: 27.9127
Evaluate side-chains
  104 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 132 optimal weight:    8.9990
   chunk 107 optimal weight:   20.0000
   chunk 68 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   overall best weight:    6.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.051252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.031416 restraints weight = 146667.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.031860 restraints weight = 85998.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.032058 restraints weight = 64195.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.032385 restraints weight = 56143.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.032478 restraints weight = 50474.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.103  15830  Z= 0.287
  Angle     :  0.701  12.379  22591  Z= 0.394
  Chirality :  0.040   0.179   2540
  Planarity :  0.005   0.060   1858
  Dihedral  : 30.262 176.843   4405
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.25), residues: 1105
  helix:  1.28 (0.19), residues: 689
  sheet: -1.41 (0.70), residues: 52
  loop : -1.98 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 497 
 TYR   0.039   0.002   TYR K 346 
 PHE   0.014   0.002   PHE K 473 
 TRP   0.009   0.002   TRP K 331 
 HIS   0.007   0.002   HIS K 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 (15829)
  covalent geometry    : angle       0.70055 (22591)
  hydrogen bonds       : bond        0.08079 (  889)
  hydrogen bonds       : angle       3.97597 ( 2267)
  metal coordination   : bond        0.00031 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9317 (mt-10)
REVERT: A   56 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8784 (mmmt)
REVERT: A   97 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8470 (mt-10)
REVERT: B   25 ASN cc_start: 0.8890 (m-40) cc_final: 0.8410 (t0)
REVERT: B   84 MET cc_start: 0.8657 (mmp) cc_final: 0.8183 (mmt)
REVERT: B   88 TYR cc_start: 0.9276 (m-80) cc_final: 0.8948 (m-80)
REVERT: D  102 LEU cc_start: 0.9554 (mm) cc_final: 0.9342 (mm)
REVERT: E  100 LEU cc_start: 0.9563 (tp) cc_final: 0.9355 (tp)
REVERT: E  106 ASP cc_start: 0.9320 (m-30) cc_final: 0.9082 (m-30)
REVERT: F   84 MET cc_start: 0.9453 (mmm) cc_final: 0.9191 (mmm)
REVERT: G   38 ASN cc_start: 0.8982 (m110) cc_final: 0.8415 (p0)
REVERT: G   99 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8505 (mmmt)
REVERT: H   71 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9041 (tm-30)
REVERT: H   93 GLU cc_start: 0.9240 (mp0) cc_final: 0.8838 (mp0)
REVERT: H  108 LYS cc_start: 0.9505 (mmtm) cc_final: 0.9106 (ptmm)
REVERT: K  201 TYR cc_start: 0.4070 (m-10) cc_final: 0.3758 (m-10)
REVERT: K  215 MET cc_start: 0.6669 (mtt) cc_final: 0.6413 (mpp)
REVERT: K  369 HIS cc_start: 0.6501 (p-80) cc_final: 0.5741 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1234
  time to fit residues: 24.9368
Evaluate side-chains
  96 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 91 optimal weight:    8.9990
   chunk 81 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 122 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  63 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS
** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 467 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.052172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.032433 restraints weight = 144343.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.032948 restraints weight = 84295.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.033279 restraints weight = 61884.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.033447 restraints weight = 52082.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.033514 restraints weight = 47753.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.4871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15830  Z= 0.183
  Angle     :  0.619  10.061  22591  Z= 0.356
  Chirality :  0.037   0.151   2540
  Planarity :  0.004   0.057   1858
  Dihedral  : 30.353 174.466   4405
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.26), residues: 1105
  helix:  1.62 (0.20), residues: 689
  sheet: -1.14 (0.74), residues: 50
  loop : -1.76 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  92 
 TYR   0.023   0.002   TYR B  88 
 PHE   0.019   0.002   PHE B  61 
 TRP   0.009   0.001   TRP K 331 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (15829)
  covalent geometry    : angle       0.61861 (22591)
  hydrogen bonds       : bond        0.05050 (  889)
  hydrogen bonds       : angle       3.66706 ( 2267)
  metal coordination   : bond        0.00058 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9592 (mt-10) cc_final: 0.9321 (pt0)
REVERT: A   55 GLN cc_start: 0.8979 (mt0) cc_final: 0.8277 (tt0)
REVERT: A   56 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8713 (mmmt)
REVERT: B   25 ASN cc_start: 0.8849 (m-40) cc_final: 0.8472 (t0)
REVERT: D  102 LEU cc_start: 0.9640 (mm) cc_final: 0.9418 (mm)
REVERT: E  106 ASP cc_start: 0.9347 (m-30) cc_final: 0.9077 (m-30)
REVERT: E  120 MET cc_start: 0.9218 (mmm) cc_final: 0.8937 (mmm)
REVERT: F   59 LYS cc_start: 0.9511 (tppp) cc_final: 0.9277 (tppp)
REVERT: F   84 MET cc_start: 0.9408 (mmm) cc_final: 0.9169 (mmm)
REVERT: G   51 LEU cc_start: 0.9578 (tp) cc_final: 0.9316 (pp)
REVERT: G   99 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8482 (mmmt)
REVERT: H   71 GLU cc_start: 0.9417 (tm-30) cc_final: 0.8933 (tm-30)
REVERT: K  201 TYR cc_start: 0.3898 (m-10) cc_final: 0.2886 (m-10)
REVERT: K  215 MET cc_start: 0.6498 (mtt) cc_final: 0.6238 (mpp)
REVERT: K  424 LYS cc_start: 0.2575 (mptt) cc_final: 0.2353 (pptt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1269
  time to fit residues: 25.4589
Evaluate side-chains
  97 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 59 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 126 optimal weight:    6.9990
   chunk 135 optimal weight:    0.0670
   chunk 51 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    4.0126

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

Flipped N/Q/H residues before XYZ refinement:
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.051717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.032007 restraints weight = 144597.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.032536 restraints weight = 84374.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.032712 restraints weight = 62032.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.033061 restraints weight = 54089.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.033185 restraints weight = 48831.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.5296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089  15830  Z= 0.205
  Angle     :  0.623  10.783  22591  Z= 0.357
  Chirality :  0.037   0.212   2540
  Planarity :  0.004   0.057   1858
  Dihedral  : 30.261 176.206   4405
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.26), residues: 1105
  helix:  1.70 (0.20), residues: 687
  sheet: -0.96 (0.75), residues: 51
  loop : -1.70 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  92 
 TYR   0.041   0.002   TYR B  88 
 PHE   0.013   0.002   PHE E 104 
 TRP   0.007   0.001   TRP K 331 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (15829)
  covalent geometry    : angle       0.62291 (22591)
  hydrogen bonds       : bond        0.05773 (  889)
  hydrogen bonds       : angle       3.66383 ( 2267)
  metal coordination   : bond        0.00011 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9592 (mt-10) cc_final: 0.9331 (pt0)
REVERT: A   55 GLN cc_start: 0.8995 (mt0) cc_final: 0.8352 (tt0)
REVERT: A   56 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8691 (mmmt)
REVERT: A   97 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8435 (mt-10)
REVERT: B   25 ASN cc_start: 0.8900 (m-40) cc_final: 0.8539 (t0)
REVERT: B   61 PHE cc_start: 0.9427 (t80) cc_final: 0.9213 (t80)
REVERT: B   84 MET cc_start: 0.8620 (tpp) cc_final: 0.8260 (tpp)
REVERT: E   90 MET cc_start: 0.8740 (tmm) cc_final: 0.8454 (tmm)
REVERT: E  106 ASP cc_start: 0.9384 (m-30) cc_final: 0.9126 (m-30)
REVERT: E  120 MET cc_start: 0.9230 (mmm) cc_final: 0.8996 (mmm)
REVERT: F   59 LYS cc_start: 0.9583 (tppp) cc_final: 0.9324 (tppp)
REVERT: F   84 MET cc_start: 0.9409 (mmm) cc_final: 0.9173 (mmm)
REVERT: G   51 LEU cc_start: 0.9600 (tp) cc_final: 0.9399 (pp)
REVERT: G   99 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8424 (mmmt)
REVERT: H   71 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8907 (tm-30)
REVERT: H   93 GLU cc_start: 0.9290 (mp0) cc_final: 0.9084 (mp0)
REVERT: H  108 LYS cc_start: 0.9438 (mmtm) cc_final: 0.9025 (ptmm)
REVERT: K  215 MET cc_start: 0.6456 (mtt) cc_final: 0.6192 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1332
  time to fit residues: 24.9309
Evaluate side-chains
  97 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 53 optimal weight:    0.0870
   chunk 111 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    4.0166

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 ASN
** K 377 ASN ** 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 = 0.3312 r_free = 0.3312 target = 0.051672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.031972 restraints weight = 143065.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.032513 restraints weight = 83605.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.032776 restraints weight = 61214.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.032861 restraints weight = 51729.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.033049 restraints weight = 48353.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15830  Z= 0.200
  Angle     :  0.620   9.578  22591  Z= 0.356
  Chirality :  0.037   0.172   2540
  Planarity :  0.004   0.060   1858
  Dihedral  : 30.334 176.273   4405
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 1105
  helix:  1.78 (0.20), residues: 687
  sheet: -1.16 (0.75), residues: 51
  loop : -1.64 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG K 161 
 TYR   0.033   0.002   TYR B  88 
 PHE   0.017   0.002   PHE E 104 
 TRP   0.008   0.001   TRP K 331 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (15829)
  covalent geometry    : angle       0.62012 (22591)
  hydrogen bonds       : bond        0.05383 (  889)
  hydrogen bonds       : angle       3.67248 ( 2267)
  metal coordination   : bond        0.00019 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9604 (mt-10) cc_final: 0.9363 (mt-10)
REVERT: A   56 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8668 (mmmt)
REVERT: A  120 MET cc_start: 0.7803 (mtp) cc_final: 0.7485 (mtp)
REVERT: B   25 ASN cc_start: 0.8938 (m-40) cc_final: 0.8555 (t0)
REVERT: B   61 PHE cc_start: 0.9454 (t80) cc_final: 0.9232 (t80)
REVERT: B   68 ASP cc_start: 0.9340 (m-30) cc_final: 0.9109 (m-30)
REVERT: B   84 MET cc_start: 0.8705 (tpp) cc_final: 0.8414 (tpp)
REVERT: E   90 MET cc_start: 0.8827 (tmm) cc_final: 0.8566 (tmm)
REVERT: E  106 ASP cc_start: 0.9365 (m-30) cc_final: 0.9146 (m-30)
REVERT: E  120 MET cc_start: 0.9235 (mmm) cc_final: 0.8977 (mmm)
REVERT: F   84 MET cc_start: 0.9394 (mmm) cc_final: 0.9177 (mmm)
REVERT: G   51 LEU cc_start: 0.9603 (tp) cc_final: 0.9387 (pp)
REVERT: G   99 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8432 (mmmt)
REVERT: H   71 GLU cc_start: 0.9428 (tm-30) cc_final: 0.8920 (tm-30)
REVERT: K  215 MET cc_start: 0.6402 (mtt) cc_final: 0.6159 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1304
  time to fit residues: 25.3666
Evaluate side-chains
  93 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 134 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 110 optimal weight:   20.0000
   chunk 105 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
K 250 HIS
** K 377 ASN ** 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 = 0.3328 r_free = 0.3328 target = 0.052225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.032634 restraints weight = 143011.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.033136 restraints weight = 82835.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.033312 restraints weight = 60311.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.033648 restraints weight = 52517.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.033759 restraints weight = 47224.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.5830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15830  Z= 0.163
  Angle     :  0.600   7.477  22591  Z= 0.345
  Chirality :  0.036   0.168   2540
  Planarity :  0.004   0.062   1858
  Dihedral  : 30.245 177.717   4405
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.26), residues: 1105
  helix:  1.84 (0.20), residues: 688
  sheet: -0.96 (0.79), residues: 51
  loop : -1.62 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 161 
 TYR   0.024   0.001   TYR B  88 
 PHE   0.015   0.001   PHE E 104 
 TRP   0.010   0.001   TRP K 331 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (15829)
  covalent geometry    : angle       0.60046 (22591)
  hydrogen bonds       : bond        0.04527 (  889)
  hydrogen bonds       : angle       3.53829 ( 2267)
  metal coordination   : bond        0.00349 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9344 (mt-10)
REVERT: A   56 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8657 (mmmt)
REVERT: A   97 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8131 (mp0)
REVERT: B   25 ASN cc_start: 0.8840 (m-40) cc_final: 0.8312 (m110)
REVERT: B   61 PHE cc_start: 0.9406 (t80) cc_final: 0.9179 (t80)
REVERT: B   68 ASP cc_start: 0.9314 (m-30) cc_final: 0.9090 (m-30)
REVERT: B   84 MET cc_start: 0.8684 (tpp) cc_final: 0.8361 (tpp)
REVERT: C   39 TYR cc_start: 0.9223 (m-80) cc_final: 0.8501 (m-80)
REVERT: E   90 MET cc_start: 0.8846 (tmm) cc_final: 0.8585 (tmm)
REVERT: E  106 ASP cc_start: 0.9409 (m-30) cc_final: 0.9157 (m-30)
REVERT: E  120 MET cc_start: 0.9247 (mmm) cc_final: 0.8985 (mmm)
REVERT: G   51 LEU cc_start: 0.9588 (tp) cc_final: 0.9333 (pp)
REVERT: G   99 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8377 (mmmt)
REVERT: H   71 GLU cc_start: 0.9397 (tm-30) cc_final: 0.8889 (tm-30)
REVERT: H   93 GLU cc_start: 0.9375 (mp0) cc_final: 0.9156 (mp0)
REVERT: K  215 MET cc_start: 0.6419 (mtt) cc_final: 0.6105 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1254
  time to fit residues: 25.2461
Evaluate side-chains
  97 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 116 optimal weight:    7.9990
   chunk 124 optimal weight:    0.6980
   chunk 120 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 132 optimal weight:   30.0000
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
K 250 HIS
** K 377 ASN ** 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 = 0.3303 r_free = 0.3303 target = 0.051235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.031682 restraints weight = 146913.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.032195 restraints weight = 85450.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.032507 restraints weight = 62252.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 67)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.032706 restraints weight = 52424.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.032812 restraints weight = 47900.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.6070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  15830  Z= 0.228
  Angle     :  0.643   8.296  22591  Z= 0.368
  Chirality :  0.038   0.201   2540
  Planarity :  0.005   0.066   1858
  Dihedral  : 30.292 178.365   4405
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 1105
  helix:  1.74 (0.20), residues: 688
  sheet: -0.96 (0.80), residues: 51
  loop : -1.62 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 128 
 TYR   0.025   0.002   TYR B  88 
 PHE   0.019   0.002   PHE H  65 
 TRP   0.007   0.001   TRP K 431 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (15829)
  covalent geometry    : angle       0.64293 (22591)
  hydrogen bonds       : bond        0.06319 (  889)
  hydrogen bonds       : angle       3.77805 ( 2267)
  metal coordination   : bond        0.00040 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9359 (mt-10)
REVERT: A   56 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8675 (mmmt)
REVERT: B   25 ASN cc_start: 0.8931 (m-40) cc_final: 0.8358 (m110)
REVERT: B   31 LYS cc_start: 0.9477 (tptp) cc_final: 0.9158 (tptt)
REVERT: B   68 ASP cc_start: 0.9367 (m-30) cc_final: 0.9151 (m-30)
REVERT: B   84 MET cc_start: 0.8740 (tpp) cc_final: 0.8438 (tpp)
REVERT: C   39 TYR cc_start: 0.9170 (m-80) cc_final: 0.8480 (m-80)
REVERT: E  106 ASP cc_start: 0.9417 (m-30) cc_final: 0.9199 (m-30)
REVERT: E  120 MET cc_start: 0.9181 (mmm) cc_final: 0.8944 (mmm)
REVERT: G   78 ILE cc_start: 0.9500 (pt) cc_final: 0.8997 (mm)
REVERT: G   99 LYS cc_start: 0.9042 (mtmm) cc_final: 0.8361 (mmmt)
REVERT: H   71 GLU cc_start: 0.9401 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: K  215 MET cc_start: 0.6431 (mtt) cc_final: 0.6157 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1326
  time to fit residues: 25.2736
Evaluate side-chains
  93 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 125 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 131 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 53 optimal weight:   30.0000
   chunk 44 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 250 HIS
** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.050769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.031376 restraints weight = 146762.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.031880 restraints weight = 86122.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.032154 restraints weight = 62803.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.032347 restraints weight = 53392.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.032419 restraints weight = 48582.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.6457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  15830  Z= 0.239
  Angle     :  0.661   8.286  22591  Z= 0.377
  Chirality :  0.039   0.204   2540
  Planarity :  0.005   0.057   1858
  Dihedral  : 30.597 178.761   4405
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.26), residues: 1105
  helix:  1.61 (0.20), residues: 688
  sheet: -1.03 (0.79), residues: 51
  loop : -1.56 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 497 
 TYR   0.028   0.002   TYR B  88 
 PHE   0.028   0.002   PHE E 104 
 TRP   0.011   0.002   TRP K 431 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (15829)
  covalent geometry    : angle       0.66067 (22591)
  hydrogen bonds       : bond        0.06575 (  889)
  hydrogen bonds       : angle       3.90168 ( 2267)
  metal coordination   : bond        0.00015 (    1)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9367 (mt-10)
REVERT: B   25 ASN cc_start: 0.8966 (m-40) cc_final: 0.8367 (m110)
REVERT: B   31 LYS cc_start: 0.9515 (tptp) cc_final: 0.9085 (tptp)
REVERT: B   68 ASP cc_start: 0.9386 (m-30) cc_final: 0.9171 (m-30)
REVERT: C   39 TYR cc_start: 0.9243 (m-80) cc_final: 0.8485 (m-80)
REVERT: E  106 ASP cc_start: 0.9437 (m-30) cc_final: 0.9229 (m-30)
REVERT: E  120 MET cc_start: 0.9192 (mmm) cc_final: 0.8952 (mmm)
REVERT: G   78 ILE cc_start: 0.9511 (pt) cc_final: 0.9036 (mm)
REVERT: G   99 LYS cc_start: 0.9029 (mtmm) cc_final: 0.8348 (mmmt)
REVERT: H   46 LYS cc_start: 0.9434 (mmtt) cc_final: 0.8638 (tppt)
REVERT: H   52 THR cc_start: 0.8741 (m) cc_final: 0.8317 (p)
REVERT: H   71 GLU cc_start: 0.9415 (tm-30) cc_final: 0.8928 (tm-30)
REVERT: K  215 MET cc_start: 0.6361 (mtt) cc_final: 0.6092 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1263
  time to fit residues: 24.1557
Evaluate side-chains
  90 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 24 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 128 optimal weight:   40.0000
   chunk 38 optimal weight:    2.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 250 HIS
** K 377 ASN ** 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 = 0.3324 r_free = 0.3324 target = 0.052111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.032334 restraints weight = 143427.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.032818 restraints weight = 84385.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.033119 restraints weight = 61767.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.033210 restraints weight = 52585.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.033210 restraints weight = 49131.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.6547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15830  Z= 0.157
  Angle     :  0.619   8.630  22591  Z= 0.353
  Chirality :  0.037   0.173   2540
  Planarity :  0.004   0.052   1858
  Dihedral  : 30.488 179.842   4405
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.61 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1105
  helix:  1.75 (0.20), residues: 688
  sheet: -0.90 (0.81), residues: 51
  loop : -1.53 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 497 
 TYR   0.026   0.001   TYR B  88 
 PHE   0.021   0.002   PHE E 104 
 TRP   0.009   0.001   TRP K 331 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (15829)
  covalent geometry    : angle       0.61873 (22591)
  hydrogen bonds       : bond        0.04499 (  889)
  hydrogen bonds       : angle       3.63823 ( 2267)
  metal coordination   : bond        0.00044 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2935.12 seconds
wall clock time: 51 minutes 11.14 seconds (3071.14 seconds total)