Starting phenix.real_space_refine
on Thu Jun  4 04:41:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r91_53848/06_2026/9r91_53848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r91_53848/06_2026/9r91_53848.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r91_53848/06_2026/9r91_53848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r91_53848/06_2026/9r91_53848.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r91_53848/06_2026/9r91_53848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r91_53848/06_2026/9r91_53848.cif"
  }
  resolution = 3.7
  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: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    6826      2.51       5
     N    1673      2.21       5
     O    1771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10323
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1861
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 16, 'TRANS': 219}
    Chain: "C"
      Number of atoms: 1796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1796
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 15, 'TRANS': 212}
    Chain: "B"
      Number of atoms: 1805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1805
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 16, 'TRANS': 212}
    Chain: "D"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 453
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
    Chain: "E"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 401
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "F"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 436
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 2, 'TRANS': 53}
    Chain: "G"
      Number of atoms: 3571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3571
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 38, 'TRANS': 417}
          Chain breaks: 1
  Time building chain proxies: 2.51, per 1000 atoms: 0.24
  Number of scatterers: 10323
  At special positions: 0
  Unit cell: (101.76, 102.82, 130.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1771      8.00
     N    1673      7.00
     C    6826      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 405.1 milliseconds
  

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2470

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      61.0% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 35
      removed outlier: 3.836A  pdb=" N   HIS A  12 " --> pdb=" O   PRO A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 51
      Proline residue:  A  48  - end of helix
    Processing helix  chain 'A' and resid 65 through 83
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 83 through 96
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 100 through 128
      Proline residue:  A 109  - end of helix
    Processing helix  chain 'A' and resid 128 through 138
      removed outlier: 3.974A  pdb=" N   LEU A 132 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 182
      Proline residue:  A 172  - end of helix
    Processing helix  chain 'A' and resid 185 through 206
      Proline residue:  A 194  - end of helix
    Processing helix  chain 'A' and resid 211 through 237
      removed outlier: 3.613A  pdb=" N   GLN A 215 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'C' and resid 9 through 35
    Processing helix  chain 'C' and resid 37 through 53
      Proline residue:  C  48  - end of helix
    Processing helix  chain 'C' and resid 65 through 96
      Proline residue:  C  71  - end of helix
      Proline residue:  C  85  - end of helix
    Processing helix  chain 'C' and resid 100 through 139
      Proline residue:  C 109  - end of helix
      removed outlier: 4.567A  pdb=" N   PHE C 130 " --> pdb=" O   TYR C 126 " (cutoff:3.500A)
      Proline residue:  C 131  - end of helix
    Processing helix  chain 'C' and resid 150 through 181
      Proline residue:  C 172  - end of helix
    Processing helix  chain 'C' and resid 185 through 207
      removed outlier: 3.592A  pdb=" N   LEU C 189 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
      Proline residue:  C 194  - end of helix
    Processing helix  chain 'C' and resid 211 through 233
      removed outlier: 3.529A  pdb=" N   GLN C 215 " --> pdb=" O   ASP C 211 " (cutoff:3.500A)
      Proline residue:  C 221  - end of helix
    Processing helix  chain 'B' and resid 8 through 35
    Processing helix  chain 'B' and resid 37 through 53
      Proline residue:  B  48  - end of helix
    Processing helix  chain 'B' and resid 65 through 83
      Proline residue:  B  71  - end of helix
    Processing helix  chain 'B' and resid 83 through 96
    Processing helix  chain 'B' and resid 97 through 99
      No H-bonds generated for 'chain 'B' and resid 97 through 99'
    Processing helix  chain 'B' and resid 100 through 128
      Proline residue:  B 109  - end of helix
    Processing helix  chain 'B' and resid 129 through 140
      removed outlier: 4.357A  pdb=" N   GLY B 135 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 182
      Proline residue:  B 172  - end of helix
    Processing helix  chain 'B' and resid 185 through 192
    Processing helix  chain 'B' and resid 192 through 207
    Processing helix  chain 'B' and resid 211 through 235
      Proline residue:  B 221  - end of helix
    Processing helix  chain 'D' and resid 5 through 21
    Processing helix  chain 'D' and resid 23 through 58
    Processing helix  chain 'E' and resid 5 through 21
    Processing helix  chain 'E' and resid 24 through 52
    Processing helix  chain 'F' and resid 5 through 19
    Processing helix  chain 'F' and resid 23 through 57
      removed outlier: 4.462A  pdb=" N   VAL F  27 " --> pdb=" O   GLN F  23 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 4 through 17
    Processing helix  chain 'G' and resid 109 through 113
    Processing helix  chain 'G' and resid 115 through 119
      removed outlier: 3.500A  pdb=" N   MET G 119 " --> pdb=" O   PRO G 116 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 148 through 155
    Processing helix  chain 'G' and resid 300 through 310
    Processing helix  chain 'G' and resid 414 through 418
    Processing helix  chain 'G' and resid 452 through 459
    Processing sheet with id=AA1, first strand: chain 'C' and resid 145 through 147
      removed outlier: 6.581A  pdb=" N   MET A  59 " --> pdb=" O   GLN C 146 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   THR A  58 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   THR A 149 " --> pdb=" O   THR A  58 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 60 through 61
    Processing sheet with id=AA3, first strand: chain 'G' and resid 39 through 41
      removed outlier: 6.673A  pdb=" N   THR G  78 " --> pdb=" O   LEU G  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 65 through 70
    Processing sheet with id=AA5, first strand: chain 'G' and resid 65 through 70
    Processing sheet with id=AA6, first strand: chain 'G' and resid 211 through 214
      removed outlier: 6.496A  pdb=" N   LEU G 282 " --> pdb=" O   VAL G 254 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   VAL G 254 " --> pdb=" O   LEU G 282 " (cutoff:3.500A)
      removed outlier: 9.587A  pdb=" N   ASP G 284 " --> pdb=" O   LEU G 252 " (cutoff:3.500A)
      removed outlier: 10.093A  pdb=" N   LEU G 252 " --> pdb=" O   ASP G 284 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER G 256 " --> pdb=" O   ALA G 264 " (cutoff:3.500A)
      removed outlier: 10.392A  pdb=" N   ALA G 264 " --> pdb=" O   SER G 256 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 221 through 224
      removed outlier: 6.217A  pdb=" N   VAL G 222 " --> pdb=" O   ARG G 324 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LEU G 319 " --> pdb=" O   CYS G 295 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   CYS G 295 " --> pdb=" O   LEU G 319 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU G 321 " --> pdb=" O   ILE G 293 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 353 through 358
      removed outlier: 6.617A  pdb=" N   ARG G 354 " --> pdb=" O   THR G 387 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ARG G 389 " --> pdb=" O   ARG G 354 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE G 356 " --> pdb=" O   ARG G 389 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   ASP G 391 " --> pdb=" O   ILE G 356 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   LEU G 358 " --> pdb=" O   ASP G 391 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   VAL G 376 " --> pdb=" O   LEU G 465 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   ASN G 467 " --> pdb=" O   VAL G 376 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ALA G 378 " --> pdb=" O   ASN G 467 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 353 through 358
      removed outlier: 6.617A  pdb=" N   ARG G 354 " --> pdb=" O   THR G 387 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ARG G 389 " --> pdb=" O   ARG G 354 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE G 356 " --> pdb=" O   ARG G 389 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   ASP G 391 " --> pdb=" O   ILE G 356 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   LEU G 358 " --> pdb=" O   ASP G 391 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   GLU G 392 " --> pdb=" O   VAL G 426 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL G 426 " --> pdb=" O   GLU G 392 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   GLN G 394 " --> pdb=" O   VAL G 424 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL G 424 " --> pdb=" O   GLN G 394 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLN G 429 " --> pdb=" O   VAL G 408 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   VAL G 408 " --> pdb=" O   GLN G 429 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   GLU G 431 " --> pdb=" O   ARG G 406 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET G 402 " --> pdb=" O   TYR G 435 " (cutoff:3.500A)

    673 hydrogen bonds defined for protein.
    1968 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3155
        1.34 -     1.46: 2133
        1.46 -     1.58: 5215
        1.58 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 10595
  Sorted by residual:
  bond pdb=" CA  SER C 233 "
       pdb=" C   SER C 233 "
    ideal  model  delta    sigma   weight residual
    1.523  1.567 -0.044 1.80e-02 3.09e+03 5.94e+00
  bond pdb=" C   PRO A 209 "
       pdb=" N   PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.339  1.401 -0.062 3.40e-02 8.65e+02 3.35e+00
  bond pdb=" C   ILE C 220 "
       pdb=" N   PRO C 221 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.36e-02 5.41e+03 2.14e+00
  bond pdb=" C   PHE C 130 "
       pdb=" N   PRO C 131 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 2.04e+00
  bond pdb=" CA  ARG C 193 "
       pdb=" C   ARG C 193 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.00e-02 1.00e+04 1.86e+00
  ... (remaining 10590 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 14202
        2.42 -     4.83: 202
        4.83 -     7.25: 48
        7.25 -     9.66: 8
        9.66 -    12.08: 3
  Bond angle restraints: 14463
  Sorted by residual:
  angle pdb=" C   LYS C 192 "
        pdb=" N   ARG C 193 "
        pdb=" CA  ARG C 193 "
      ideal   model   delta    sigma   weight residual
     121.62  128.84   -7.22 1.57e+00 4.06e-01 2.12e+01
  angle pdb=" C   ASP A 211 "
        pdb=" N   VAL A 212 "
        pdb=" CA  VAL A 212 "
      ideal   model   delta    sigma   weight residual
     120.60  126.27   -5.67 1.29e+00 6.01e-01 1.93e+01
  angle pdb=" N   VAL B 171 "
        pdb=" CA  VAL B 171 "
        pdb=" C   VAL B 171 "
      ideal   model   delta    sigma   weight residual
     108.88  116.93   -8.05 2.16e+00 2.14e-01 1.39e+01
  angle pdb=" C   GLN A  52 "
        pdb=" N   LEU A  53 "
        pdb=" CA  LEU A  53 "
      ideal   model   delta    sigma   weight residual
     120.51  125.71   -5.20 1.45e+00 4.76e-01 1.29e+01
  angle pdb=" N   GLY G 110 "
        pdb=" CA  GLY G 110 "
        pdb=" C   GLY G 110 "
      ideal   model   delta    sigma   weight residual
     112.34  119.63   -7.29 2.04e+00 2.40e-01 1.28e+01
  ... (remaining 14458 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 5710
       17.67 -    35.35: 432
       35.35 -    53.02: 96
       53.02 -    70.69: 22
       70.69 -    88.36: 7
  Dihedral angle restraints: 6267
    sinusoidal: 2452
      harmonic: 3815
  Sorted by residual:
  dihedral pdb=" CA  PRO A  67 "
           pdb=" C   PRO A  67 "
           pdb=" N   PHE A  68 "
           pdb=" CA  PHE A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ASN B 139 "
           pdb=" C   ASN B 139 "
           pdb=" N   THR B 140 "
           pdb=" CA  THR B 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.94   18.06     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ILE A  95 "
           pdb=" C   ILE A  95 "
           pdb=" N   ALA A  96 "
           pdb=" CA  ALA A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.19  -17.81     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 6264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1112
       0.036 -    0.073: 397
       0.073 -    0.109: 139
       0.109 -    0.146: 47
       0.146 -    0.182: 13
  Chirality restraints: 1708
  Sorted by residual:
  chirality pdb=" CB  ILE A  41 "
            pdb=" CA  ILE A  41 "
            pdb=" CG1 ILE A  41 "
            pdb=" CG2 ILE A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.32e-01
  chirality pdb=" CA  GLN D  23 "
            pdb=" N   GLN D  23 "
            pdb=" C   GLN D  23 "
            pdb=" CB  GLN D  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.58e-01
  chirality pdb=" CA  THR C  70 "
            pdb=" N   THR C  70 "
            pdb=" C   THR C  70 "
            pdb=" CB  THR C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 7.09e-01
  ... (remaining 1705 not shown)

  Planarity restraints: 1806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G 108 "   -0.042 5.00e-02 4.00e+02   6.41e-02 6.57e+00
        pdb=" N   PRO G 109 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO G 109 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO G 109 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  75 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   THR A  75 "    0.044 2.00e-02 2.50e+03
        pdb=" O   THR A  75 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PHE A  76 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  91 "    0.013 2.00e-02 2.50e+03   2.53e-02 6.42e+00
        pdb=" C   VAL A  91 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL A  91 "    0.016 2.00e-02 2.50e+03
        pdb=" N   TRP A  92 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1803 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1405
        2.76 -     3.29: 10026
        3.29 -     3.83: 17980
        3.83 -     4.36: 19184
        4.36 -     4.90: 33800
  Nonbonded interactions: 82395
  Sorted by model distance:
  nonbonded pdb=" N   GLY G 381 "
            pdb=" O   PHE G 436 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   ILE B  81 "
            pdb=" OH  TYR B 119 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OG  SER B  57 "
            pdb=" O   VAL B 147 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   ILE C  81 "
            pdb=" OH  TYR C 119 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   GLY B 204 "
            pdb=" OG1 THR B 208 "
     model   vdw
     2.318 3.040
  ... (remaining 82390 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 8 through 235)
  selection = (chain 'B' and resid 8 through 235)
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and resid 2 through 52)
  selection = (chain 'E' and resid 2 through 52)
  selection = (chain 'F' and resid 2 through 52)
}

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:             6.520
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.620
  Find NCS groups from input model:        0.130
  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:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10595  Z= 0.196
  Angle     :  0.793  12.079  14463  Z= 0.414
  Chirality :  0.047   0.182   1708
  Planarity :  0.007   0.064   1806
  Dihedral  : 13.720  88.364   3797
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.54 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.51 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.22), residues: 1299
  helix:  0.86 (0.18), residues: 752
  sheet: -0.58 (0.42), residues: 142
  loop : -0.88 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G 278 
 TYR   0.015   0.002   TYR B 100 
 PHE   0.023   0.001   PHE G 448 
 TRP   0.016   0.002   TRP A  92 
 HIS   0.005   0.001   HIS A 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.20 (10595)
  covalent geometry    : angle       0.79312 /  0.41 (14463)
  hydrogen bonds       : bond        0.11569 /  7.92 (  662)
  hydrogen bonds       : angle       5.85425 /  4.22 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 242
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7466 (tt0)
REVERT: A   16 LEU cc_start: 0.9166 (tp) cc_final: 0.8888 (tt)
REVERT: A  181 MET cc_start: 0.7473 (tmm) cc_final: 0.7248 (tmm)
REVERT: A  205 MET cc_start: 0.8497 (tpp) cc_final: 0.8238 (ttm)
REVERT: C   40 ASP cc_start: 0.8690 (m-30) cc_final: 0.8450 (t70)
REVERT: C  205 MET cc_start: 0.8794 (mtm) cc_final: 0.8547 (mtt)
REVERT: C  227 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5727 (mm-30)
REVERT: G  338 MET cc_start: 0.8935 (mpp) cc_final: 0.7141 (ppp)
  outliers start: 18
  outliers final: 1
  residues processed: 256
  average time/residue: 0.1071
  time to fit residues: 37.5229
Evaluate side-chains
  172 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 170
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain B residue   35 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0060
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 102 HIS
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  57 GLN
G  10 GLN
G  53 GLN
G 187 GLN
G 238 ASN
G 394 GLN
G 404 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.122269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.099093 restraints weight = 27195.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.100341 restraints weight = 13898.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.100164 restraints weight = 8869.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.100472 restraints weight = 9561.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.100725 restraints weight = 8349.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10595  Z= 0.139
  Angle     :  0.665  11.030  14463  Z= 0.323
  Chirality :  0.042   0.154   1708
  Planarity :  0.005   0.056   1806
  Dihedral  :  5.328  66.095   1412
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.39 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.14 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.23), residues: 1299
  helix:  1.67 (0.18), residues: 759
  sheet: -0.37 (0.42), residues: 149
  loop : -0.64 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 304 
 TYR   0.015   0.002   TYR B  42 
 PHE   0.019   0.001   PHE C 124 
 TRP   0.011   0.001   TRP G 161 
 HIS   0.009   0.001   HIS A  12 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.14 (10595)
  covalent geometry    : angle       0.66531 /  0.32 (14463)
  hydrogen bonds       : bond        0.04218 /  2.81 (  662)
  hydrogen bonds       : angle       4.70365 /  3.42 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.9043 (tp) cc_final: 0.8801 (tt)
REVERT: C  190 ARG cc_start: 0.6630 (tmm-80) cc_final: 0.6359 (tmm-80)
REVERT: C  205 MET cc_start: 0.8325 (mtm) cc_final: 0.7973 (mtt)
REVERT: B  211 ASP cc_start: 0.7315 (t0) cc_final: 0.6696 (p0)
REVERT: F    8 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6790 (mt-10)
REVERT: G  338 MET cc_start: 0.8461 (mpp) cc_final: 0.7212 (ppp)
REVERT: G  404 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7622 (pm20)
  outliers start: 26
  outliers final: 14
  residues processed: 201
  average time/residue: 0.1096
  time to fit residues: 30.4746
Evaluate side-chains
  183 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   90 ILE
Chi-restraints excluded: chain G residue  160 MET
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  404 GLN
Chi-restraints excluded: chain G residue  443 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 121 optimal weight:    0.0980
   chunk 112 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.124236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.101754 restraints weight = 28213.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.102938 restraints weight = 13786.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.103383 restraints weight = 9551.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.103607 restraints weight = 9571.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.103622 restraints weight = 8366.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10595  Z= 0.149
  Angle     :  0.678  13.191  14463  Z= 0.326
  Chirality :  0.042   0.196   1708
  Planarity :  0.005   0.057   1806
  Dihedral  :  4.463  36.502   1409
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.84 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.24), residues: 1299
  helix:  1.92 (0.18), residues: 761
  sheet: -0.49 (0.41), residues: 159
  loop : -0.65 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G 232 
 TYR   0.016   0.002   TYR C 223 
 PHE   0.027   0.001   PHE F  13 
 TRP   0.012   0.001   TRP G 420 
 HIS   0.003   0.001   HIS A  12 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 (10595)
  covalent geometry    : angle       0.67753 /  0.33 (14463)
  hydrogen bonds       : bond        0.04040 /  2.70 (  662)
  hydrogen bonds       : angle       4.58758 /  3.33 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 183
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.8966 (tp) cc_final: 0.8723 (tt)
REVERT: A  122 MET cc_start: 0.8583 (mtt) cc_final: 0.8344 (mtt)
REVERT: A  195 TYR cc_start: 0.6135 (m-80) cc_final: 0.5653 (m-10)
REVERT: C   63 ASP cc_start: 0.8140 (m-30) cc_final: 0.7786 (t0)
REVERT: C  190 ARG cc_start: 0.6752 (tmm-80) cc_final: 0.6491 (tmm-80)
REVERT: C  205 MET cc_start: 0.8064 (mtm) cc_final: 0.7682 (mtt)
REVERT: B  211 ASP cc_start: 0.7113 (t0) cc_final: 0.6862 (p0)
REVERT: E    7 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8023 (t)
REVERT: E    9 LEU cc_start: 0.8589 (tp) cc_final: 0.8262 (pp)
REVERT: F    8 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6516 (mt-10)
REVERT: G  160 MET cc_start: 0.6864 (mmm) cc_final: 0.6408 (mmm)
REVERT: G  338 MET cc_start: 0.8312 (mpp) cc_final: 0.7180 (ppp)
REVERT: G  404 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7326 (pm20)
  outliers start: 30
  outliers final: 17
  residues processed: 206
  average time/residue: 0.1031
  time to fit residues: 29.8022
Evaluate side-chains
  186 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  232 ARG
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  404 GLN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 115 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 118 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 238 ASN
G 404 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.123074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.100524 restraints weight = 28267.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.101252 restraints weight = 14474.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.101355 restraints weight = 9892.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.101456 restraints weight = 10130.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.101528 restraints weight = 9004.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10595  Z= 0.155
  Angle     :  0.661  13.290  14463  Z= 0.321
  Chirality :  0.042   0.155   1708
  Planarity :  0.005   0.059   1806
  Dihedral  :  4.392  37.914   1409
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.28 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.24), residues: 1299
  helix:  2.01 (0.18), residues: 761
  sheet: -0.43 (0.41), residues: 160
  loop : -0.70 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 232 
 TYR   0.019   0.002   TYR G 141 
 PHE   0.032   0.001   PHE F  13 
 TRP   0.011   0.001   TRP C 180 
 HIS   0.003   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 (10595)
  covalent geometry    : angle       0.66080 /  0.32 (14463)
  hydrogen bonds       : bond        0.03977 /  2.65 (  662)
  hydrogen bonds       : angle       4.51362 /  3.28 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 185
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.8952 (tp) cc_final: 0.8729 (tt)
REVERT: A  195 TYR cc_start: 0.6302 (m-80) cc_final: 0.5808 (m-10)
REVERT: C   53 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8624 (mp)
REVERT: C   63 ASP cc_start: 0.8178 (m-30) cc_final: 0.7916 (t0)
REVERT: C  190 ARG cc_start: 0.6954 (tmm-80) cc_final: 0.6557 (tmm-80)
REVERT: C  205 MET cc_start: 0.8077 (mtm) cc_final: 0.7705 (ttt)
REVERT: B  211 ASP cc_start: 0.7247 (t0) cc_final: 0.6906 (p0)
REVERT: E    7 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8006 (t)
REVERT: E    9 LEU cc_start: 0.8601 (tp) cc_final: 0.8173 (pp)
REVERT: F    8 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6732 (mt-10)
REVERT: G  160 MET cc_start: 0.6907 (mmm) cc_final: 0.6287 (mmm)
REVERT: G  338 MET cc_start: 0.8425 (mpp) cc_final: 0.7300 (ppp)
REVERT: G  404 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7350 (pm20)
  outliers start: 36
  outliers final: 21
  residues processed: 213
  average time/residue: 0.1051
  time to fit residues: 31.4861
Evaluate side-chains
  195 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  232 ARG
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  404 GLN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0270
   chunk 110 optimal weight:   10.0000
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 187 GLN
G 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.122921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.097798 restraints weight = 28008.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.100224 restraints weight = 14065.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.101648 restraints weight = 9049.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.102472 restraints weight = 7006.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.102885 restraints weight = 6118.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10595  Z= 0.147
  Angle     :  0.662  12.516  14463  Z= 0.319
  Chirality :  0.042   0.166   1708
  Planarity :  0.005   0.065   1806
  Dihedral  :  4.371  38.246   1409
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 18.19 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.24), residues: 1299
  helix:  2.06 (0.18), residues: 760
  sheet: -0.39 (0.41), residues: 160
  loop : -0.66 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 232 
 TYR   0.016   0.002   TYR A  42 
 PHE   0.018   0.001   PHE G 448 
 TRP   0.015   0.001   TRP C 180 
 HIS   0.003   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 (10595)
  covalent geometry    : angle       0.66237 /  0.32 (14463)
  hydrogen bonds       : bond        0.03915 /  2.61 (  662)
  hydrogen bonds       : angle       4.46552 /  3.25 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 186
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 TYR cc_start: 0.6153 (m-80) cc_final: 0.5686 (m-10)
REVERT: C   53 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8606 (mp)
REVERT: C  190 ARG cc_start: 0.6961 (tmm-80) cc_final: 0.6630 (tmm-80)
REVERT: E    7 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8029 (t)
REVERT: E    9 LEU cc_start: 0.8512 (tp) cc_final: 0.8186 (pp)
REVERT: G  160 MET cc_start: 0.6873 (mmm) cc_final: 0.6242 (mmm)
REVERT: G  338 MET cc_start: 0.8406 (mpp) cc_final: 0.7316 (ppp)
  outliers start: 42
  outliers final: 28
  residues processed: 216
  average time/residue: 0.1001
  time to fit residues: 30.2436
Evaluate side-chains
  201 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 171
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   90 ILE
Chi-restraints excluded: chain G residue  187 GLN
Chi-restraints excluded: chain G residue  212 LEU
Chi-restraints excluded: chain G residue  232 ARG
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 113 optimal weight:    0.0670
   chunk 84 optimal weight:    0.0870
   chunk 88 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 187 GLN
G 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.123514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.101431 restraints weight = 28184.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.101335 restraints weight = 16093.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.101817 restraints weight = 10486.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.102052 restraints weight = 10516.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.102254 restraints weight = 8983.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10595  Z= 0.128
  Angle     :  0.671  12.784  14463  Z= 0.318
  Chirality :  0.042   0.189   1708
  Planarity :  0.005   0.071   1806
  Dihedral  :  4.336  37.975   1409
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.86 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.24), residues: 1299
  helix:  2.12 (0.18), residues: 760
  sheet: -0.42 (0.41), residues: 162
  loop : -0.58 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 232 
 TYR   0.017   0.002   TYR G 177 
 PHE   0.034   0.001   PHE F  13 
 TRP   0.014   0.001   TRP G  82 
 HIS   0.002   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 (10595)
  covalent geometry    : angle       0.67087 /  0.32 (14463)
  hydrogen bonds       : bond        0.03754 /  2.51 (  662)
  hydrogen bonds       : angle       4.37483 /  3.17 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 182
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 TYR cc_start: 0.6271 (m-80) cc_final: 0.5824 (m-10)
REVERT: C   53 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8577 (mp)
REVERT: C  190 ARG cc_start: 0.7052 (tmm-80) cc_final: 0.6784 (tmm-80)
REVERT: E    7 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.7960 (t)
REVERT: E    9 LEU cc_start: 0.8509 (tp) cc_final: 0.8151 (pp)
REVERT: F   55 LYS cc_start: 0.5332 (pttm) cc_final: 0.4807 (tppt)
REVERT: G  160 MET cc_start: 0.6965 (mmm) cc_final: 0.6479 (mmm)
REVERT: G  246 MET cc_start: 0.6846 (mmm) cc_final: 0.6636 (mmm)
REVERT: G  338 MET cc_start: 0.8303 (mpp) cc_final: 0.7211 (ppp)
  outliers start: 31
  outliers final: 21
  residues processed: 201
  average time/residue: 0.1009
  time to fit residues: 28.6365
Evaluate side-chains
  192 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  187 GLN
Chi-restraints excluded: chain G residue  212 LEU
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 92 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.119634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.095482 restraints weight = 26557.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.096227 restraints weight = 14927.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.096833 restraints weight = 10436.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.097053 restraints weight = 8647.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.097299 restraints weight = 8448.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10595  Z= 0.150
  Angle     :  0.697  12.700  14463  Z= 0.329
  Chirality :  0.043   0.203   1708
  Planarity :  0.005   0.077   1806
  Dihedral  :  4.336  39.528   1409
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.21 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.24), residues: 1299
  helix:  2.09 (0.18), residues: 760
  sheet: -0.48 (0.40), residues: 165
  loop : -0.51 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 232 
 TYR   0.018   0.002   TYR G 177 
 PHE   0.036   0.001   PHE F  13 
 TRP   0.011   0.001   TRP G 425 
 HIS   0.003   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (10595)
  covalent geometry    : angle       0.69692 /  0.33 (14463)
  hydrogen bonds       : bond        0.03852 /  2.57 (  662)
  hydrogen bonds       : angle       4.38186 /  3.17 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 178
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 TYR cc_start: 0.6592 (m-80) cc_final: 0.6142 (m-10)
REVERT: C   53 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8680 (mp)
REVERT: C  170 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7790 (mm-30)
REVERT: C  190 ARG cc_start: 0.7101 (tmm-80) cc_final: 0.6789 (tmm-80)
REVERT: E    7 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7876 (t)
REVERT: E    9 LEU cc_start: 0.8527 (tp) cc_final: 0.8161 (pp)
REVERT: F   55 LYS cc_start: 0.5341 (pttm) cc_final: 0.4884 (tppt)
REVERT: G  160 MET cc_start: 0.6944 (mmm) cc_final: 0.6452 (mmm)
REVERT: G  232 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.5557 (tpp80)
REVERT: G  338 MET cc_start: 0.8495 (mpp) cc_final: 0.7231 (ppp)
  outliers start: 39
  outliers final: 26
  residues processed: 207
  average time/residue: 0.1039
  time to fit residues: 30.3227
Evaluate side-chains
  193 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  187 GLN
Chi-restraints excluded: chain G residue  212 LEU
Chi-restraints excluded: chain G residue  232 ARG
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 187 GLN
** G 238 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 = 0.3896 r_free = 0.3896 target = 0.118759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.095984 restraints weight = 26843.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.096075 restraints weight = 14367.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.095998 restraints weight = 10843.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.096236 restraints weight = 10743.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.096741 restraints weight = 9406.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10595  Z= 0.157
  Angle     :  0.728  12.802  14463  Z= 0.348
  Chirality :  0.044   0.225   1708
  Planarity :  0.005   0.068   1806
  Dihedral  :  4.347  40.514   1409
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.47 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.24), residues: 1299
  helix:  2.06 (0.18), residues: 760
  sheet: -0.51 (0.41), residues: 157
  loop : -0.63 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  54 
 TYR   0.025   0.002   TYR G 177 
 PHE   0.036   0.001   PHE C 124 
 TRP   0.012   0.001   TRP G 425 
 HIS   0.003   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 (10595)
  covalent geometry    : angle       0.72827 /  0.35 (14463)
  hydrogen bonds       : bond        0.03920 /  2.61 (  662)
  hydrogen bonds       : angle       4.43535 /  3.20 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 176
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   90 GLN cc_start: 0.7453 (mt0) cc_final: 0.7038 (mt0)
REVERT: C  190 ARG cc_start: 0.7167 (tmm-80) cc_final: 0.6910 (tmm-80)
REVERT: E    7 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.7870 (t)
REVERT: E    9 LEU cc_start: 0.8528 (tp) cc_final: 0.8165 (pp)
REVERT: F   55 LYS cc_start: 0.5285 (pttm) cc_final: 0.4867 (tppt)
REVERT: G  160 MET cc_start: 0.6957 (mmm) cc_final: 0.6469 (mmm)
REVERT: G  338 MET cc_start: 0.8475 (mpp) cc_final: 0.7263 (ppp)
  outliers start: 40
  outliers final: 33
  residues processed: 203
  average time/residue: 0.1006
  time to fit residues: 28.8350
Evaluate side-chains
  202 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 168
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  195 TYR
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   90 ILE
Chi-restraints excluded: chain G residue  187 GLN
Chi-restraints excluded: chain G residue  212 LEU
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Chi-restraints excluded: chain G residue  444 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 107 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 187 GLN
G 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.118042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.094369 restraints weight = 26987.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095386 restraints weight = 14377.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095465 restraints weight = 9915.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.095905 restraints weight = 10183.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.095852 restraints weight = 9720.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10595  Z= 0.170
  Angle     :  0.739  12.218  14463  Z= 0.353
  Chirality :  0.044   0.228   1708
  Planarity :  0.005   0.059   1806
  Dihedral  :  4.393  42.066   1409
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.23 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.91 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.24), residues: 1299
  helix:  2.03 (0.18), residues: 759
  sheet: -0.44 (0.42), residues: 153
  loop : -0.74 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G 232 
 TYR   0.018   0.002   TYR A  42 
 PHE   0.044   0.001   PHE C 124 
 TRP   0.014   0.001   TRP G 425 
 HIS   0.003   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 (10595)
  covalent geometry    : angle       0.73859 /  0.35 (14463)
  hydrogen bonds       : bond        0.04044 /  2.69 (  662)
  hydrogen bonds       : angle       4.46190 /  3.21 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 ARG cc_start: 0.7250 (tmm-80) cc_final: 0.6999 (tmm-80)
REVERT: E    7 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.7906 (t)
REVERT: E    9 LEU cc_start: 0.8552 (tp) cc_final: 0.8183 (pp)
REVERT: F   55 LYS cc_start: 0.5206 (pttm) cc_final: 0.4841 (tppt)
REVERT: G  160 MET cc_start: 0.6980 (mmm) cc_final: 0.6528 (mmm)
REVERT: G  338 MET cc_start: 0.8345 (mpp) cc_final: 0.7235 (ppp)
  outliers start: 35
  outliers final: 32
  residues processed: 200
  average time/residue: 0.0964
  time to fit residues: 27.8256
Evaluate side-chains
  199 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   90 ILE
Chi-restraints excluded: chain G residue  187 GLN
Chi-restraints excluded: chain G residue  212 LEU
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Chi-restraints excluded: chain G residue  444 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 123 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 108 optimal weight:    8.9990
   chunk 38 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A   7 GLN
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 187 GLN
G 238 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.118786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.094683 restraints weight = 27291.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.095913 restraints weight = 14770.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.095887 restraints weight = 9493.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.096149 restraints weight = 10046.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.096433 restraints weight = 8882.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10595  Z= 0.147
  Angle     :  0.733  13.867  14463  Z= 0.347
  Chirality :  0.043   0.263   1708
  Planarity :  0.005   0.055   1806
  Dihedral  :  4.358  41.907   1409
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.91 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.24), residues: 1299
  helix:  2.07 (0.18), residues: 759
  sheet: -0.48 (0.42), residues: 153
  loop : -0.68 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 234 
 TYR   0.019   0.002   TYR A  42 
 PHE   0.045   0.001   PHE C 124 
 TRP   0.015   0.001   TRP G 425 
 HIS   0.002   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 (10595)
  covalent geometry    : angle       0.73335 /  0.35 (14463)
  hydrogen bonds       : bond        0.03922 /  2.62 (  662)
  hydrogen bonds       : angle       4.41014 /  3.18 ( 1968)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 169
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 ARG cc_start: 0.7334 (tmm-80) cc_final: 0.7075 (tmm-80)
REVERT: D   37 ARG cc_start: 0.8423 (tpm170) cc_final: 0.7890 (tpm170)
REVERT: E    7 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.7815 (t)
REVERT: E    9 LEU cc_start: 0.8496 (tp) cc_final: 0.8141 (pp)
REVERT: F   55 LYS cc_start: 0.5310 (pttm) cc_final: 0.4939 (tppt)
REVERT: G  160 MET cc_start: 0.6966 (mmm) cc_final: 0.6486 (mmm)
REVERT: G  246 MET cc_start: 0.6354 (mmm) cc_final: 0.6088 (mmm)
REVERT: G  338 MET cc_start: 0.8505 (mpp) cc_final: 0.7324 (ppp)
  outliers start: 37
  outliers final: 33
  residues processed: 194
  average time/residue: 0.0904
  time to fit residues: 25.3463
Evaluate side-chains
  198 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  195 TYR
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain D residue    2 PHE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   90 ILE
Chi-restraints excluded: chain G residue  130 LEU
Chi-restraints excluded: chain G residue  187 GLN
Chi-restraints excluded: chain G residue  212 LEU
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  238 ASN
Chi-restraints excluded: chain G residue  424 VAL
Chi-restraints excluded: chain G residue  443 HIS
Chi-restraints excluded: chain G residue  444 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 119 optimal weight:    0.4980
   chunk 69 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 109 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0020
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
A   7 GLN
** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 187 GLN
G 238 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.118832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.095403 restraints weight = 27225.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.096367 restraints weight = 13999.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.096610 restraints weight = 10047.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.096866 restraints weight = 9979.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.096891 restraints weight = 9037.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10595  Z= 0.144
  Angle     :  0.728  13.622  14463  Z= 0.344
  Chirality :  0.043   0.262   1708
  Planarity :  0.005   0.053   1806
  Dihedral  :  4.322  41.636   1409
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.27 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.24), residues: 1299
  helix:  2.10 (0.18), residues: 759
  sheet: -0.54 (0.42), residues: 155
  loop : -0.63 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 234 
 TYR   0.021   0.002   TYR A 154 
 PHE   0.044   0.001   PHE C 124 
 TRP   0.015   0.001   TRP G 425 
 HIS   0.002   0.001   HIS G 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.14 (10595)
  covalent geometry    : angle       0.72771 /  0.34 (14463)
  hydrogen bonds       : bond        0.03908 /  2.60 (  662)
  hydrogen bonds       : angle       4.39461 /  3.16 ( 1968)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1916.90 seconds
wall clock time: 33 minutes 48.52 seconds (2028.52 seconds total)