Starting phenix.real_space_refine
on Fri Aug 22 22:01:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hii_34817/08_2025/8hii_34817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hii_34817/08_2025/8hii_34817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hii_34817/08_2025/8hii_34817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hii_34817/08_2025/8hii_34817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hii_34817/08_2025/8hii_34817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hii_34817/08_2025/8hii_34817.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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      26      5.16       5
     C    5284      2.51       5
     N    1372      2.21       5
     O    1530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8212
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3969
          Classifications: {'peptide': 498}
          Link IDs: {'PTRANS': 17, 'TRANS': 480}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1686
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
    Chain: "N"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1632
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201}
  Time building chain proxies: 2.22, per 1000 atoms: 0.27
  Number of scatterers: 8212
  At special positions: 0
  Unit cell: (66.34, 101.65, 150.87, 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      26     16.00
     O    1530      8.00
     N    1372      7.00
     C    5284      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03

  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: 0.67
  Conformation dependent library (CDL) restraints added in 494.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1972

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      40.8% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid -80 through -64
    Processing helix  chain 'A' and resid -58 through -43
      removed outlier: 3.785A  pdb=" N   ALA A -54 " --> pdb=" O   GLN A -58 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA A -43 " --> pdb=" O   ALA A -47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -38 through -33
      removed outlier: 4.211A  pdb=" N   ASP A -33 " --> pdb=" O   PRO A -37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -25 through -3
      removed outlier: 3.805A  pdb=" N   ARG A -21 " --> pdb=" O   MET A -25 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A  -5 " --> pdb=" O   ASP A  -9 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN A  -3 " --> pdb=" O   LEU A  -7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2 through 18
    Processing helix  chain 'A' and resid 27 through 39
      removed outlier: 3.793A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET A  38 " --> pdb=" O   PHE A  34 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A  39 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 67 through 90
      removed outlier: 3.828A  pdb=" N   VAL A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 4.702A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 112
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.755A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 144
      removed outlier: 3.685A  pdb=" N   SER A 138 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 176
    Processing helix  chain 'A' and resid 181 through 202
      removed outlier: 3.736A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 259
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 4.108A  pdb=" N   TYR A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 323
    Processing helix  chain 'A' and resid 333 through 354
      removed outlier: 4.657A  pdb=" N   LEU A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A 338 " --> pdb=" O   TRP A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 378
      removed outlier: 3.845A  pdb=" N   ALA A 367 " --> pdb=" O   TRP A 363 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 386
    Processing helix  chain 'A' and resid 392 through 419
    Processing helix  chain 'A' and resid 427 through 451
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.508A  pdb=" N   ASP H  93 " --> pdb=" O   ARG H  90 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 90 through 94'
    Processing helix  chain 'H' and resid 107 through 112
      removed outlier: 3.889A  pdb=" N   TRP H 111 " --> pdb=" O   GLY H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 170 through 172
      No H-bonds generated for 'chain 'H' and resid 170 through 172'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.530A  pdb=" N   ASP N  90 " --> pdb=" O   LYS N  87 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 87 through 91'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.967A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 125 through 130
    Processing helix  chain 'L' and resid 184 through 188
      removed outlier: 3.543A  pdb=" N   ASP L 187 " --> pdb=" O   SER L 184 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR L 188 " --> pdb=" O   LYS L 185 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 184 through 188'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15
      removed outlier: 6.785A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.134A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.134A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168
      removed outlier: 4.237A  pdb=" N   TYR H 208 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12
      removed outlier: 4.154A  pdb=" N   THR N 118 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.612A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   VAL N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   MET N  34 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   TYR N 110 " --> pdb=" O   ILE N  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AB1, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.594A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN L  91 " --> pdb=" O   THR L  99 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.594A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 120
      removed outlier: 3.679A  pdb=" N   ASN L 139 " --> pdb=" O   SER L 116 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 147 through 148
      removed outlier: 3.668A  pdb=" N   LYS L 147 " --> pdb=" O   THR L 199 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 151 through 152

    438 hydrogen bonds defined for protein.
    1233 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: 1.39

  Time building geometry restraints manager: 0.92 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: 2560
        1.34 -     1.46: 2052
        1.46 -     1.58: 3763
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 8413
  Sorted by residual:
  bond pdb=" C   VAL A  81 "
       pdb=" N   PRO A  82 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.97e+00
  bond pdb=" C   LYS H 215 "
       pdb=" N   PRO H 216 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.32e+00
  bond pdb=" CA  LYS L 185 "
       pdb=" C   LYS L 185 "
    ideal  model  delta    sigma   weight residual
    1.522  1.555 -0.033 1.72e-02 3.38e+03 3.75e+00
  bond pdb=" C   SER L   8 "
       pdb=" N   PRO L   9 "
    ideal  model  delta    sigma   weight residual
    1.334  1.377 -0.043 2.34e-02 1.83e+03 3.38e+00
  bond pdb=" C   THR A  93 "
       pdb=" N   PRO A  94 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.020 1.25e-02 6.40e+03 2.45e+00
  ... (remaining 8408 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 11059
        1.84 -     3.68: 304
        3.68 -     5.52: 51
        5.52 -     7.36: 21
        7.36 -     9.20: 9
  Bond angle restraints: 11444
  Sorted by residual:
  angle pdb=" N   THR A  69 "
        pdb=" CA  THR A  69 "
        pdb=" C   THR A  69 "
      ideal   model   delta    sigma   weight residual
     109.81  118.52   -8.71 2.21e+00 2.05e-01 1.55e+01
  angle pdb=" C   ASN L 212 "
        pdb=" N   ARG L 213 "
        pdb=" CA  ARG L 213 "
      ideal   model   delta    sigma   weight residual
     121.70  127.96   -6.26 1.80e+00 3.09e-01 1.21e+01
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.63   -6.09 1.91e+00 2.74e-01 1.02e+01
  angle pdb=" C   PHE N 103 "
        pdb=" N   TYR N 104 "
        pdb=" CA  TYR N 104 "
      ideal   model   delta    sigma   weight residual
     122.46  126.93   -4.47 1.41e+00 5.03e-01 1.01e+01
  angle pdb=" CA  GLU H 108 "
        pdb=" C   GLU H 108 "
        pdb=" N   PRO H 109 "
      ideal   model   delta    sigma   weight residual
     118.44  123.03   -4.59 1.59e+00 3.96e-01 8.33e+00
  ... (remaining 11439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.22: 4753
       15.22 -    30.44: 149
       30.44 -    45.65: 44
       45.65 -    60.87: 0
       60.87 -    76.09: 11
  Dihedral angle restraints: 4957
    sinusoidal: 1880
      harmonic: 3077
  Sorted by residual:
  dihedral pdb=" CB  CYS H 154 "
           pdb=" SG  CYS H 154 "
           pdb=" SG  CYS H 210 "
           pdb=" CB  CYS H 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.09  -76.09     1      1.00e+01 1.00e-02 7.29e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.40   23.60     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  ASN A -61 "
           pdb=" C   ASN A -61 "
           pdb=" N   ALA A -60 "
           pdb=" CA  ALA A -60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.18  -20.82     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 4954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 936
       0.049 -    0.097: 283
       0.097 -    0.146: 68
       0.146 -    0.194: 7
       0.194 -    0.243: 2
  Chirality restraints: 1296
  Sorted by residual:
  chirality pdb=" CA  THR A  69 "
            pdb=" N   THR A  69 "
            pdb=" C   THR A  69 "
            pdb=" CB  THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  THR A  69 "
            pdb=" CA  THR A  69 "
            pdb=" OG1 THR A  69 "
            pdb=" CG2 THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CB  ILE A 134 "
            pdb=" CA  ILE A 134 "
            pdb=" CG1 ILE A 134 "
            pdb=" CG2 ILE A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.40e-01
  ... (remaining 1293 not shown)

  Planarity restraints: 1435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 102 "   -0.015 2.00e-02 2.50e+03   1.39e-02 4.83e+00
        pdb=" CG  TRP H 102 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 102 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 102 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 102 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 102 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 102 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 102 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 102 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 102 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 108 "   -0.033 5.00e-02 4.00e+02   4.87e-02 3.80e+00
        pdb=" N   PRO H 109 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO H 109 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 109 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  59 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.25e+00
        pdb=" N   PRO L  60 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO L  60 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO L  60 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1432 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1930
        2.79 -     3.32: 7029
        3.32 -     3.84: 13294
        3.84 -     4.37: 14915
        4.37 -     4.90: 26285
  Nonbonded interactions: 63453
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 168 "
            pdb=" O   GLY A 307 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   VAL A  83 "
            pdb=" OG1 THR A  87 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OD2 ASP H  76 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   ASP L 187 "
            pdb=" OH  TYR L 194 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   TRP H 111 "
            pdb=" OH  TYR L  92 "
     model   vdw
     2.351 3.040
  ... (remaining 63448 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.770
  Find NCS groups from input model:        0.040
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
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   0.052   8418  Z= 0.185
  Angle     :  0.804   9.205  11454  Z= 0.432
  Chirality :  0.048   0.243   1296
  Planarity :  0.006   0.049   1435
  Dihedral  :  9.451  75.332   2970
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -3.43 (0.21), residues: 1045
  helix: -1.94 (0.20), residues: 374
  sheet: -1.97 (0.29), residues: 262
  loop : -2.61 (0.27), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  62 
 TYR   0.026   0.002   TYR A  74 
 PHE   0.028   0.002   PHE A 103 
 TRP   0.037   0.002   TRP H 102 
 HIS   0.008   0.002   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8413)
  covalent geometry    : angle       0.80323 (11444)
  SS BOND              : bond        0.00163 (    5)
  SS BOND              : angle       1.19226 (   10)
  hydrogen bonds       : bond        0.13641 (  414)
  hydrogen bonds       : angle       6.84550 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7694 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8142 (tttt) cc_final: 0.7881 (mttt)
REVERT: A  -35 LEU cc_start: 0.7218 (tt) cc_final: 0.6988 (tt)
REVERT: A  -26 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6787 (mt-10)
REVERT: A   41 ILE cc_start: 0.7252 (mt) cc_final: 0.6985 (mt)
REVERT: A   42 ARG cc_start: 0.5848 (mtm110) cc_final: 0.5496 (ptp90)
REVERT: A   61 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7381 (ttp-110)
REVERT: A   79 VAL cc_start: 0.8003 (m) cc_final: 0.7726 (t)
REVERT: A  133 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7138 (mmm160)
REVERT: A  152 VAL cc_start: 0.7831 (t) cc_final: 0.7624 (p)
REVERT: A  290 ILE cc_start: 0.7986 (mt) cc_final: 0.7491 (tt)
REVERT: A  382 ILE cc_start: 0.8056 (mt) cc_final: 0.7674 (mt)
REVERT: A  399 VAL cc_start: 0.6954 (t) cc_final: 0.6518 (p)
REVERT: A  404 THR cc_start: 0.8137 (m) cc_final: 0.7670 (p)
REVERT: A  408 THR cc_start: 0.8008 (m) cc_final: 0.7575 (p)
REVERT: A  411 LYS cc_start: 0.7719 (ttpt) cc_final: 0.7396 (ttpt)
REVERT: A  428 VAL cc_start: 0.7597 (p) cc_final: 0.6889 (t)
REVERT: A  434 LEU cc_start: 0.7925 (tp) cc_final: 0.7711 (tp)
REVERT: H   28 SER cc_start: 0.8035 (p) cc_final: 0.7764 (t)
REVERT: H  130 THR cc_start: 0.7891 (p) cc_final: 0.7608 (t)
REVERT: N   34 MET cc_start: 0.6133 (mtp) cc_final: 0.5913 (mtp)
REVERT: N   89 GLU cc_start: 0.6957 (mp0) cc_final: 0.6222 (mp0)
REVERT: L   43 LYS cc_start: 0.8732 (mttt) cc_final: 0.8479 (mtmm)
REVERT: L   46 LYS cc_start: 0.8008 (mttm) cc_final: 0.7779 (mttm)
REVERT: L  111 THR cc_start: 0.8670 (p) cc_final: 0.8426 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0991
  time to fit residues: 32.7652
Evaluate side-chains
  204 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.1980
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A -42 GLN
A   5 GLN
A 277 ASN
A 293 ASN
A 386 GLN
A 431 GLN
H  42 GLN
** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  65 GLN
L  39 GLN
L 200 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.140769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.123258 restraints weight = 13138.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.127009 restraints weight = 6760.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.129434 restraints weight = 4158.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.131126 restraints weight = 2897.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.132121 restraints weight = 2193.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8418  Z= 0.186
  Angle     :  0.599   5.977  11454  Z= 0.314
  Chirality :  0.043   0.170   1296
  Planarity :  0.004   0.037   1435
  Dihedral  :  4.614  19.750   1153
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  8.17 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -1.71 (0.25), residues: 1045
  helix: -0.03 (0.25), residues: 386
  sheet: -1.16 (0.31), residues: 245
  loop : -2.12 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  67 
 TYR   0.020   0.002   TYR L  50 
 PHE   0.013   0.002   PHE A 103 
 TRP   0.032   0.002   TRP H 102 
 HIS   0.006   0.002   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8413)
  covalent geometry    : angle       0.59824 (11444)
  SS BOND              : bond        0.00306 (    5)
  SS BOND              : angle       1.43723 (   10)
  hydrogen bonds       : bond        0.04385 (  414)
  hydrogen bonds       : angle       4.93698 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 218
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7958 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8144 (tttt) cc_final: 0.7712 (mttm)
REVERT: A  -35 LEU cc_start: 0.7356 (tt) cc_final: 0.7142 (tt)
REVERT: A  -26 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7058 (mt-10)
REVERT: A  -24 LYS cc_start: 0.7708 (mttt) cc_final: 0.7462 (mttp)
REVERT: A   42 ARG cc_start: 0.6234 (mtm110) cc_final: 0.5966 (mtm-85)
REVERT: A   88 ASP cc_start: 0.6635 (m-30) cc_final: 0.6349 (m-30)
REVERT: A   95 VAL cc_start: 0.7714 (p) cc_final: 0.7483 (t)
REVERT: A  126 TYR cc_start: 0.7786 (t80) cc_final: 0.7532 (t80)
REVERT: A  133 ARG cc_start: 0.7574 (mmt180) cc_final: 0.7331 (mtp85)
REVERT: A  152 VAL cc_start: 0.8055 (t) cc_final: 0.7853 (p)
REVERT: A  276 PHE cc_start: 0.7192 (m-10) cc_final: 0.6992 (m-80)
REVERT: A  310 ASP cc_start: 0.6860 (t0) cc_final: 0.6494 (m-30)
REVERT: A  346 GLN cc_start: 0.7825 (mt0) cc_final: 0.7562 (tt0)
REVERT: A  361 SER cc_start: 0.7507 (m) cc_final: 0.7297 (p)
REVERT: A  393 LYS cc_start: 0.8363 (mttt) cc_final: 0.8159 (mttt)
REVERT: A  404 THR cc_start: 0.8439 (m) cc_final: 0.8044 (p)
REVERT: A  408 THR cc_start: 0.8408 (m) cc_final: 0.7967 (t)
REVERT: A  434 LEU cc_start: 0.8112 (tp) cc_final: 0.7887 (tp)
REVERT: H   24 SER cc_start: 0.8288 (m) cc_final: 0.7759 (t)
REVERT: H   74 SER cc_start: 0.7668 (t) cc_final: 0.7229 (p)
REVERT: H  116 TYR cc_start: 0.7917 (m-10) cc_final: 0.7694 (m-80)
REVERT: H  130 THR cc_start: 0.8189 (p) cc_final: 0.7969 (t)
REVERT: H  177 VAL cc_start: 0.8385 (t) cc_final: 0.8135 (p)
REVERT: N   83 MET cc_start: 0.6011 (ttm) cc_final: 0.5650 (ttm)
REVERT: N   89 GLU cc_start: 0.6779 (mp0) cc_final: 0.6316 (mp0)
REVERT: N   95 TYR cc_start: 0.7763 (m-10) cc_final: 0.7546 (m-80)
REVERT: L   43 LYS cc_start: 0.8829 (mttt) cc_final: 0.8531 (mtmm)
REVERT: L   46 LYS cc_start: 0.8050 (mttm) cc_final: 0.7724 (mttm)
  outliers start: 23
  outliers final: 9
  residues processed: 228
  average time/residue: 0.0972
  time to fit residues: 29.9201
Evaluate side-chains
  214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 205
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   chunk 102 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   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 -70 ASN
A -42 GLN
A 277 ASN
H 169 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 191 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.137544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.119947 restraints weight = 13106.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.123662 restraints weight = 6666.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.126223 restraints weight = 4073.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.127883 restraints weight = 2820.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.128913 restraints weight = 2128.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8418  Z= 0.207
  Angle     :  0.623   6.848  11454  Z= 0.322
  Chirality :  0.044   0.134   1296
  Planarity :  0.004   0.033   1435
  Dihedral  :  4.675  19.006   1153
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 10.19 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -1.01 (0.26), residues: 1045
  helix:  0.69 (0.26), residues: 383
  sheet: -0.79 (0.33), residues: 245
  loop : -1.86 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 148 
 TYR   0.014   0.002   TYR H  63 
 PHE   0.014   0.002   PHE A  84 
 TRP   0.026   0.002   TRP H 102 
 HIS   0.006   0.002   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 8413)
  covalent geometry    : angle       0.62108 (11444)
  SS BOND              : bond        0.00342 (    5)
  SS BOND              : angle       1.59910 (   10)
  hydrogen bonds       : bond        0.04491 (  414)
  hydrogen bonds       : angle       4.91330 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7918 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8184 (tttt) cc_final: 0.7684 (mttm)
REVERT: A  -26 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6990 (mt-10)
REVERT: A  -24 LYS cc_start: 0.7830 (mttt) cc_final: 0.7476 (mttp)
REVERT: A   77 LEU cc_start: 0.7409 (tp) cc_final: 0.7199 (mt)
REVERT: A  133 ARG cc_start: 0.7595 (mmt180) cc_final: 0.7275 (mmm160)
REVERT: A  152 VAL cc_start: 0.8124 (t) cc_final: 0.7871 (p)
REVERT: A  162 LEU cc_start: 0.7902 (tp) cc_final: 0.7607 (tp)
REVERT: A  204 LYS cc_start: 0.8470 (tttt) cc_final: 0.8235 (tttt)
REVERT: A  287 TYR cc_start: 0.7847 (m-80) cc_final: 0.7493 (m-80)
REVERT: A  310 ASP cc_start: 0.7174 (t0) cc_final: 0.6890 (t0)
REVERT: A  346 GLN cc_start: 0.7730 (mt0) cc_final: 0.7441 (tt0)
REVERT: A  361 SER cc_start: 0.7736 (m) cc_final: 0.7378 (p)
REVERT: A  373 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7283 (mtp85)
REVERT: A  393 LYS cc_start: 0.8372 (mttt) cc_final: 0.8149 (mttt)
REVERT: A  404 THR cc_start: 0.8350 (m) cc_final: 0.7806 (p)
REVERT: A  408 THR cc_start: 0.8437 (m) cc_final: 0.7873 (p)
REVERT: A  434 LEU cc_start: 0.8122 (tp) cc_final: 0.7882 (tp)
REVERT: H   24 SER cc_start: 0.8517 (m) cc_final: 0.7974 (t)
REVERT: H   74 SER cc_start: 0.7829 (t) cc_final: 0.7444 (p)
REVERT: H  152 LEU cc_start: 0.7753 (tp) cc_final: 0.7506 (tp)
REVERT: H  177 VAL cc_start: 0.8474 (t) cc_final: 0.8251 (p)
REVERT: N   89 GLU cc_start: 0.6677 (mp0) cc_final: 0.6192 (mp0)
REVERT: L    6 THR cc_start: 0.8476 (t) cc_final: 0.8067 (p)
REVERT: L   46 LYS cc_start: 0.8080 (mttm) cc_final: 0.7735 (mttm)
  outliers start: 26
  outliers final: 18
  residues processed: 212
  average time/residue: 0.0971
  time to fit residues: 27.5610
Evaluate side-chains
  215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -16 ILE
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 86 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0470
   chunk 39 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A -12 GLN
A 120 GLN
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 212 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.136676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.119200 restraints weight = 13451.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.122991 restraints weight = 6842.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125515 restraints weight = 4195.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.127223 restraints weight = 2884.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128239 restraints weight = 2165.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8418  Z= 0.174
  Angle     :  0.606   9.639  11454  Z= 0.308
  Chirality :  0.043   0.225   1296
  Planarity :  0.004   0.034   1435
  Dihedral  :  4.551  19.262   1153
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 13.10 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -0.66 (0.27), residues: 1045
  helix:  1.05 (0.26), residues: 383
  sheet: -0.65 (0.33), residues: 245
  loop : -1.69 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.012   0.002   TYR A 287 
 PHE   0.013   0.001   PHE L 141 
 TRP   0.017   0.002   TRP H 102 
 HIS   0.006   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8413)
  covalent geometry    : angle       0.60522 (11444)
  SS BOND              : bond        0.00267 (    5)
  SS BOND              : angle       1.39143 (   10)
  hydrogen bonds       : bond        0.04183 (  414)
  hydrogen bonds       : angle       4.77264 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7888 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8197 (tttt) cc_final: 0.7735 (mttm)
REVERT: A  -26 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6954 (mt-10)
REVERT: A  -24 LYS cc_start: 0.7803 (mttt) cc_final: 0.7448 (mttp)
REVERT: A   98 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7264 (tp)
REVERT: A  133 ARG cc_start: 0.7597 (mmt180) cc_final: 0.7274 (mmm160)
REVERT: A  148 ARG cc_start: 0.6716 (mmm-85) cc_final: 0.6457 (mmm-85)
REVERT: A  152 VAL cc_start: 0.8107 (t) cc_final: 0.7821 (p)
REVERT: A  162 LEU cc_start: 0.7978 (tp) cc_final: 0.7688 (tp)
REVERT: A  204 LYS cc_start: 0.8493 (tttt) cc_final: 0.8264 (tttt)
REVERT: A  310 ASP cc_start: 0.7246 (t0) cc_final: 0.6880 (t0)
REVERT: A  346 GLN cc_start: 0.7717 (mt0) cc_final: 0.7411 (tt0)
REVERT: A  361 SER cc_start: 0.7744 (m) cc_final: 0.7370 (p)
REVERT: A  373 ARG cc_start: 0.7529 (mmm160) cc_final: 0.7240 (mtp85)
REVERT: A  393 LYS cc_start: 0.8330 (mttt) cc_final: 0.8028 (mttt)
REVERT: A  404 THR cc_start: 0.8320 (m) cc_final: 0.7783 (p)
REVERT: A  408 THR cc_start: 0.8428 (m) cc_final: 0.7957 (p)
REVERT: A  411 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7669 (ttpt)
REVERT: A  434 LEU cc_start: 0.8138 (tp) cc_final: 0.7868 (tp)
REVERT: H   24 SER cc_start: 0.8542 (m) cc_final: 0.8015 (t)
REVERT: H   74 SER cc_start: 0.7877 (t) cc_final: 0.7534 (p)
REVERT: H  177 VAL cc_start: 0.8490 (t) cc_final: 0.8236 (p)
REVERT: N   89 GLU cc_start: 0.6652 (mp0) cc_final: 0.6181 (mp0)
REVERT: L    6 THR cc_start: 0.8422 (t) cc_final: 0.8059 (p)
REVERT: L   46 LYS cc_start: 0.8109 (mttm) cc_final: 0.7746 (mttm)
  outliers start: 28
  outliers final: 17
  residues processed: 212
  average time/residue: 0.0916
  time to fit residues: 26.0721
Evaluate side-chains
  214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -78 ASP
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    0.3980
   chunk 70 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 2 optimal weight:    0.2980
   chunk 53 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.135018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.117821 restraints weight = 13382.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.121505 restraints weight = 6792.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.124006 restraints weight = 4163.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.125685 restraints weight = 2862.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.126694 restraints weight = 2151.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8418  Z= 0.187
  Angle     :  0.609   7.794  11454  Z= 0.312
  Chirality :  0.043   0.238   1296
  Planarity :  0.004   0.037   1435
  Dihedral  :  4.523  18.723   1153
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.01 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -0.38 (0.27), residues: 1045
  helix:  1.31 (0.27), residues: 381
  sheet: -0.48 (0.34), residues: 245
  loop : -1.57 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.012   0.002   TYR A  76 
 PHE   0.021   0.001   PHE H 114 
 TRP   0.016   0.002   TRP A  25 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 8413)
  covalent geometry    : angle       0.60786 (11444)
  SS BOND              : bond        0.00280 (    5)
  SS BOND              : angle       1.49425 (   10)
  hydrogen bonds       : bond        0.04326 (  414)
  hydrogen bonds       : angle       4.76910 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 196
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7916 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8256 (tttt) cc_final: 0.7732 (mttm)
REVERT: A  -26 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6932 (mt-10)
REVERT: A  -25 MET cc_start: 0.7202 (ttt) cc_final: 0.6738 (ttp)
REVERT: A  -24 LYS cc_start: 0.7824 (mttt) cc_final: 0.7466 (mttp)
REVERT: A   38 MET cc_start: 0.6899 (mmt) cc_final: 0.6696 (mmm)
REVERT: A   77 LEU cc_start: 0.7330 (tp) cc_final: 0.7092 (mp)
REVERT: A  133 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7335 (mmm160)
REVERT: A  148 ARG cc_start: 0.6794 (mmm-85) cc_final: 0.6523 (mmm-85)
REVERT: A  152 VAL cc_start: 0.8037 (t) cc_final: 0.7751 (p)
REVERT: A  162 LEU cc_start: 0.8004 (tp) cc_final: 0.7689 (tp)
REVERT: A  203 LEU cc_start: 0.7380 (mt) cc_final: 0.6848 (mt)
REVERT: A  310 ASP cc_start: 0.7249 (t0) cc_final: 0.6873 (t0)
REVERT: A  346 GLN cc_start: 0.7728 (mt0) cc_final: 0.7353 (tt0)
REVERT: A  373 ARG cc_start: 0.7529 (mmm160) cc_final: 0.7302 (mtp85)
REVERT: A  393 LYS cc_start: 0.8371 (mttt) cc_final: 0.8031 (mttt)
REVERT: A  404 THR cc_start: 0.8311 (m) cc_final: 0.7896 (p)
REVERT: A  408 THR cc_start: 0.8518 (m) cc_final: 0.8069 (t)
REVERT: A  409 ILE cc_start: 0.8021 (mt) cc_final: 0.7724 (mt)
REVERT: A  411 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7748 (ttpt)
REVERT: A  434 LEU cc_start: 0.8140 (tp) cc_final: 0.7920 (tp)
REVERT: H   24 SER cc_start: 0.8570 (m) cc_final: 0.8065 (t)
REVERT: H   74 SER cc_start: 0.7918 (t) cc_final: 0.7574 (p)
REVERT: H  177 VAL cc_start: 0.8457 (t) cc_final: 0.8250 (p)
REVERT: N   89 GLU cc_start: 0.6742 (mp0) cc_final: 0.6241 (mp0)
REVERT: L    6 THR cc_start: 0.8448 (t) cc_final: 0.8017 (p)
REVERT: L   37 TYR cc_start: 0.8749 (m-10) cc_final: 0.8329 (m-80)
REVERT: L   46 LYS cc_start: 0.8119 (mttm) cc_final: 0.7739 (mttm)
  outliers start: 28
  outliers final: 18
  residues processed: 207
  average time/residue: 0.0922
  time to fit residues: 25.7437
Evaluate side-chains
  211 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -78 ASP
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -34 GLU
Chi-restraints excluded: chain A residue  -16 ILE
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain H residue  197 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** 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 = 0.3672 r_free = 0.3672 target = 0.130890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.113698 restraints weight = 13138.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117318 restraints weight = 6674.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.119781 restraints weight = 4101.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.121305 restraints weight = 2845.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122434 restraints weight = 2189.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8418  Z= 0.239
  Angle     :  0.649   9.108  11454  Z= 0.334
  Chirality :  0.045   0.265   1296
  Planarity :  0.004   0.041   1435
  Dihedral  :  4.711  20.288   1153
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.24 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -0.32 (0.27), residues: 1045
  helix:  1.27 (0.27), residues: 384
  sheet: -0.32 (0.35), residues: 238
  loop : -1.53 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  52 
 TYR   0.029   0.002   TYR L  50 
 PHE   0.019   0.001   PHE H 114 
 TRP   0.020   0.002   TRP A  25 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 8413)
  covalent geometry    : angle       0.64758 (11444)
  SS BOND              : bond        0.00345 (    5)
  SS BOND              : angle       1.62164 (   10)
  hydrogen bonds       : bond        0.04697 (  414)
  hydrogen bonds       : angle       4.91908 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 197
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.8346 (tt) cc_final: 0.8130 (tt)
REVERT: A  -68 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7956 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6502 (t0) cc_final: 0.5916 (t0)
REVERT: A  -51 LYS cc_start: 0.8254 (tttt) cc_final: 0.7725 (mttm)
REVERT: A  -25 MET cc_start: 0.7422 (ttt) cc_final: 0.7002 (ttp)
REVERT: A  -24 LYS cc_start: 0.7863 (mttt) cc_final: 0.7504 (mttp)
REVERT: A   27 HIS cc_start: 0.5759 (OUTLIER) cc_final: 0.4929 (m-70)
REVERT: A   61 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7911 (ttm110)
REVERT: A   77 LEU cc_start: 0.7490 (tp) cc_final: 0.7188 (mt)
REVERT: A  112 LEU cc_start: 0.7885 (mt) cc_final: 0.7449 (pp)
REVERT: A  115 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8166 (p)
REVERT: A  133 ARG cc_start: 0.7623 (mmt180) cc_final: 0.7329 (mmm160)
REVERT: A  148 ARG cc_start: 0.6928 (mmm-85) cc_final: 0.6627 (mmm-85)
REVERT: A  152 VAL cc_start: 0.8192 (t) cc_final: 0.7901 (p)
REVERT: A  162 LEU cc_start: 0.8052 (tp) cc_final: 0.7745 (tp)
REVERT: A  203 LEU cc_start: 0.7550 (mt) cc_final: 0.7022 (mt)
REVERT: A  310 ASP cc_start: 0.7289 (t0) cc_final: 0.6959 (t0)
REVERT: A  373 ARG cc_start: 0.7523 (mmm160) cc_final: 0.7252 (mtp85)
REVERT: A  393 LYS cc_start: 0.8323 (mttt) cc_final: 0.7976 (mttt)
REVERT: A  404 THR cc_start: 0.8314 (m) cc_final: 0.7794 (p)
REVERT: A  408 THR cc_start: 0.8512 (m) cc_final: 0.8028 (p)
REVERT: A  409 ILE cc_start: 0.8066 (mt) cc_final: 0.7722 (mt)
REVERT: A  411 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7689 (ttpt)
REVERT: A  434 LEU cc_start: 0.8170 (tp) cc_final: 0.7942 (tp)
REVERT: H   24 SER cc_start: 0.8595 (m) cc_final: 0.8116 (t)
REVERT: H   74 SER cc_start: 0.7936 (t) cc_final: 0.7605 (p)
REVERT: H  131 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8011 (ttpp)
REVERT: H  177 VAL cc_start: 0.8491 (t) cc_final: 0.8268 (p)
REVERT: H  195 VAL cc_start: 0.8108 (p) cc_final: 0.7726 (m)
REVERT: N   89 GLU cc_start: 0.6760 (mp0) cc_final: 0.6233 (mp0)
REVERT: L    6 THR cc_start: 0.8453 (t) cc_final: 0.8015 (p)
REVERT: L   37 TYR cc_start: 0.8765 (m-10) cc_final: 0.8340 (m-80)
REVERT: L   46 LYS cc_start: 0.8037 (mttm) cc_final: 0.7671 (mttm)
REVERT: L  183 LEU cc_start: 0.7413 (mt) cc_final: 0.7208 (mt)
  outliers start: 31
  outliers final: 19
  residues processed: 211
  average time/residue: 0.0990
  time to fit residues: 28.2585
Evaluate side-chains
  217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -78 ASP
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -34 GLU
Chi-restraints excluded: chain A residue  -16 ILE
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  131 LYS
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain H residue  197 THR
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0010
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.134096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.116989 restraints weight = 13223.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.120667 restraints weight = 6784.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.123032 restraints weight = 4181.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.124601 restraints weight = 2926.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.125762 restraints weight = 2242.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8418  Z= 0.174
  Angle     :  0.627  11.173  11454  Z= 0.316
  Chirality :  0.044   0.245   1296
  Planarity :  0.004   0.039   1435
  Dihedral  :  4.527  19.267   1153
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.13 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -0.14 (0.28), residues: 1045
  helix:  1.40 (0.27), residues: 384
  sheet: -0.24 (0.35), residues: 243
  loop : -1.42 (0.33), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  52 
 TYR   0.028   0.002   TYR L  50 
 PHE   0.021   0.001   PHE A  84 
 TRP   0.013   0.001   TRP A -76 
 HIS   0.002   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8413)
  covalent geometry    : angle       0.62562 (11444)
  SS BOND              : bond        0.00256 (    5)
  SS BOND              : angle       1.30639 (   10)
  hydrogen bonds       : bond        0.04296 (  414)
  hydrogen bonds       : angle       4.75905 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 196
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.8302 (tt) cc_final: 0.8032 (tt)
REVERT: A  -68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7987 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8230 (tttt) cc_final: 0.7709 (mttm)
REVERT: A  -25 MET cc_start: 0.7270 (ttt) cc_final: 0.6876 (ttp)
REVERT: A  -24 LYS cc_start: 0.7777 (mttt) cc_final: 0.7437 (mttp)
REVERT: A   27 HIS cc_start: 0.5490 (OUTLIER) cc_final: 0.4948 (m-70)
REVERT: A   72 LEU cc_start: 0.8118 (tp) cc_final: 0.7835 (tt)
REVERT: A  112 LEU cc_start: 0.7865 (mt) cc_final: 0.7397 (pp)
REVERT: A  115 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8132 (p)
REVERT: A  133 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7280 (mmm160)
REVERT: A  148 ARG cc_start: 0.6906 (mmm-85) cc_final: 0.6589 (mmm-85)
REVERT: A  152 VAL cc_start: 0.8177 (t) cc_final: 0.7892 (p)
REVERT: A  162 LEU cc_start: 0.8023 (tp) cc_final: 0.7708 (tp)
REVERT: A  203 LEU cc_start: 0.7473 (mt) cc_final: 0.6941 (mt)
REVERT: A  283 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7706 (tp)
REVERT: A  310 ASP cc_start: 0.7302 (t0) cc_final: 0.6971 (t0)
REVERT: A  339 ILE cc_start: 0.7805 (mt) cc_final: 0.7492 (mt)
REVERT: A  373 ARG cc_start: 0.7480 (mmm160) cc_final: 0.7260 (mtp85)
REVERT: A  377 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7223 (mm-40)
REVERT: A  404 THR cc_start: 0.8299 (m) cc_final: 0.7780 (p)
REVERT: A  408 THR cc_start: 0.8499 (m) cc_final: 0.7930 (p)
REVERT: A  409 ILE cc_start: 0.8055 (mt) cc_final: 0.7694 (mt)
REVERT: A  434 LEU cc_start: 0.8153 (tp) cc_final: 0.7918 (tp)
REVERT: H   24 SER cc_start: 0.8589 (m) cc_final: 0.8135 (t)
REVERT: H   74 SER cc_start: 0.7954 (t) cc_final: 0.7581 (p)
REVERT: H  124 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7497 (p)
REVERT: N   89 GLU cc_start: 0.6753 (mp0) cc_final: 0.6203 (mp0)
REVERT: L    6 THR cc_start: 0.8462 (t) cc_final: 0.8007 (p)
REVERT: L   37 TYR cc_start: 0.8761 (m-10) cc_final: 0.8343 (m-80)
REVERT: L   46 LYS cc_start: 0.8021 (mttm) cc_final: 0.7680 (mttm)
REVERT: L  123 SER cc_start: 0.8017 (p) cc_final: 0.7805 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 210
  average time/residue: 0.1001
  time to fit residues: 28.4390
Evaluate side-chains
  214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -78 ASP
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -16 ILE
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain H residue   23 LEU
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0970
   chunk 9 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.129473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112060 restraints weight = 13337.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.115565 restraints weight = 6817.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.118010 restraints weight = 4243.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.119616 restraints weight = 2965.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120594 restraints weight = 2266.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8418  Z= 0.186
  Angle     :  0.646   9.944  11454  Z= 0.326
  Chirality :  0.044   0.230   1296
  Planarity :  0.004   0.039   1435
  Dihedral  :  4.535  18.634   1153
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.37 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -0.05 (0.28), residues: 1045
  helix:  1.44 (0.27), residues: 384
  sheet: -0.09 (0.35), residues: 238
  loop : -1.37 (0.33), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 253 
 TYR   0.027   0.002   TYR L  50 
 PHE   0.016   0.001   PHE H 114 
 TRP   0.014   0.001   TRP A  25 
 HIS   0.003   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8413)
  covalent geometry    : angle       0.64530 (11444)
  SS BOND              : bond        0.00277 (    5)
  SS BOND              : angle       1.42706 (   10)
  hydrogen bonds       : bond        0.04360 (  414)
  hydrogen bonds       : angle       4.73555 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7979 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6513 (t0) cc_final: 0.5904 (t0)
REVERT: A  -51 LYS cc_start: 0.8227 (tttt) cc_final: 0.7727 (mttm)
REVERT: A  -25 MET cc_start: 0.7325 (ttt) cc_final: 0.6927 (ttp)
REVERT: A  -24 LYS cc_start: 0.7806 (mttt) cc_final: 0.7449 (mttp)
REVERT: A   27 HIS cc_start: 0.5479 (OUTLIER) cc_final: 0.5018 (m-70)
REVERT: A   61 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7973 (ttm110)
REVERT: A  112 LEU cc_start: 0.7853 (mt) cc_final: 0.7409 (pp)
REVERT: A  115 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8167 (p)
REVERT: A  133 ARG cc_start: 0.7613 (mmt180) cc_final: 0.7284 (mmm160)
REVERT: A  144 VAL cc_start: 0.7812 (t) cc_final: 0.7581 (p)
REVERT: A  148 ARG cc_start: 0.6897 (mmm-85) cc_final: 0.6612 (mmm-85)
REVERT: A  152 VAL cc_start: 0.8165 (t) cc_final: 0.7884 (p)
REVERT: A  162 LEU cc_start: 0.8045 (tp) cc_final: 0.7719 (tp)
REVERT: A  203 LEU cc_start: 0.7431 (mt) cc_final: 0.6788 (tp)
REVERT: A  283 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7703 (tp)
REVERT: A  310 ASP cc_start: 0.7291 (t0) cc_final: 0.6983 (t0)
REVERT: A  339 ILE cc_start: 0.7943 (mt) cc_final: 0.7604 (mt)
REVERT: A  373 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7266 (mtp85)
REVERT: A  377 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7226 (mm-40)
REVERT: A  393 LYS cc_start: 0.8109 (mttt) cc_final: 0.7499 (mttt)
REVERT: A  404 THR cc_start: 0.8290 (m) cc_final: 0.7772 (p)
REVERT: A  408 THR cc_start: 0.8460 (m) cc_final: 0.7938 (p)
REVERT: A  409 ILE cc_start: 0.8062 (mt) cc_final: 0.7714 (mt)
REVERT: A  434 LEU cc_start: 0.8153 (tp) cc_final: 0.7927 (tp)
REVERT: H   24 SER cc_start: 0.8587 (m) cc_final: 0.8147 (t)
REVERT: H   74 SER cc_start: 0.7958 (t) cc_final: 0.7591 (p)
REVERT: H  124 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7511 (p)
REVERT: H  195 VAL cc_start: 0.8124 (p) cc_final: 0.7745 (m)
REVERT: N   83 MET cc_start: 0.6091 (ttm) cc_final: 0.5817 (ttm)
REVERT: N   89 GLU cc_start: 0.6745 (mp0) cc_final: 0.6224 (mp0)
REVERT: L    6 THR cc_start: 0.8459 (t) cc_final: 0.8001 (p)
REVERT: L   37 TYR cc_start: 0.8774 (m-10) cc_final: 0.8373 (m-80)
REVERT: L   46 LYS cc_start: 0.8017 (mttm) cc_final: 0.7679 (mttm)
  outliers start: 27
  outliers final: 20
  residues processed: 214
  average time/residue: 0.1025
  time to fit residues: 29.7476
Evaluate side-chains
  220 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -78 ASP
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -34 GLU
Chi-restraints excluded: chain A residue  -16 ILE
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    0.2980
   chunk 43 optimal weight:    0.3980
   chunk 77 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0980
   chunk 64 optimal weight:    0.4980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.131902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.114637 restraints weight = 13396.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.118243 restraints weight = 6837.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120571 restraints weight = 4219.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.122205 restraints weight = 2964.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.123311 restraints weight = 2255.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8418  Z= 0.158
  Angle     :  0.649  12.992  11454  Z= 0.323
  Chirality :  0.044   0.275   1296
  Planarity :  0.004   0.043   1435
  Dihedral  :  4.466  17.918   1153
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.92 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole:  0.00 (0.28), residues: 1045
  helix:  1.45 (0.27), residues: 385
  sheet: -0.12 (0.36), residues: 237
  loop : -1.27 (0.33), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 253 
 TYR   0.026   0.002   TYR A 149 
 PHE   0.014   0.001   PHE H 114 
 TRP   0.031   0.001   TRP A -76 
 HIS   0.003   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8413)
  covalent geometry    : angle       0.64798 (11444)
  SS BOND              : bond        0.00227 (    5)
  SS BOND              : angle       1.31320 (   10)
  hydrogen bonds       : bond        0.04189 (  414)
  hydrogen bonds       : angle       4.68855 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7921 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6491 (t0) cc_final: 0.5923 (t0)
REVERT: A  -51 LYS cc_start: 0.8242 (tttt) cc_final: 0.7759 (mttm)
REVERT: A  -25 MET cc_start: 0.7257 (ttt) cc_final: 0.6847 (ttp)
REVERT: A  -24 LYS cc_start: 0.7778 (mttt) cc_final: 0.7421 (mttp)
REVERT: A   27 HIS cc_start: 0.5440 (OUTLIER) cc_final: 0.5053 (m-70)
REVERT: A   61 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.7821 (ttm110)
REVERT: A   77 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6905 (mp)
REVERT: A  112 LEU cc_start: 0.7810 (mt) cc_final: 0.7399 (pp)
REVERT: A  133 ARG cc_start: 0.7629 (mmt180) cc_final: 0.7267 (mmm160)
REVERT: A  148 ARG cc_start: 0.6778 (mmm-85) cc_final: 0.6507 (mmm-85)
REVERT: A  149 TYR cc_start: 0.6431 (t80) cc_final: 0.5995 (t80)
REVERT: A  152 VAL cc_start: 0.8195 (t) cc_final: 0.7968 (p)
REVERT: A  162 LEU cc_start: 0.8028 (tp) cc_final: 0.7701 (tp)
REVERT: A  203 LEU cc_start: 0.7437 (mt) cc_final: 0.6819 (tp)
REVERT: A  283 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7628 (tp)
REVERT: A  310 ASP cc_start: 0.7268 (t0) cc_final: 0.6945 (t0)
REVERT: A  339 ILE cc_start: 0.7937 (mt) cc_final: 0.7605 (mt)
REVERT: A  373 ARG cc_start: 0.7447 (mmm160) cc_final: 0.7231 (mtp85)
REVERT: A  393 LYS cc_start: 0.7928 (mttt) cc_final: 0.7651 (mttt)
REVERT: A  404 THR cc_start: 0.8274 (m) cc_final: 0.7889 (p)
REVERT: A  408 THR cc_start: 0.8448 (m) cc_final: 0.8172 (t)
REVERT: A  409 ILE cc_start: 0.8046 (mt) cc_final: 0.7629 (mt)
REVERT: A  411 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7646 (ttpt)
REVERT: A  412 THR cc_start: 0.8597 (m) cc_final: 0.8330 (t)
REVERT: A  434 LEU cc_start: 0.8146 (tp) cc_final: 0.7923 (tp)
REVERT: H   24 SER cc_start: 0.8475 (m) cc_final: 0.7975 (t)
REVERT: H   74 SER cc_start: 0.7970 (t) cc_final: 0.7604 (p)
REVERT: H  124 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7483 (p)
REVERT: H  195 VAL cc_start: 0.8126 (p) cc_final: 0.7737 (m)
REVERT: N   83 MET cc_start: 0.6129 (ttm) cc_final: 0.5802 (ttm)
REVERT: N   89 GLU cc_start: 0.6739 (mp0) cc_final: 0.6230 (mp0)
REVERT: L   37 TYR cc_start: 0.8773 (m-10) cc_final: 0.8393 (m-80)
REVERT: L   46 LYS cc_start: 0.8018 (mttm) cc_final: 0.7680 (mttm)
REVERT: L  111 THR cc_start: 0.8582 (p) cc_final: 0.8255 (p)
  outliers start: 26
  outliers final: 20
  residues processed: 212
  average time/residue: 0.0985
  time to fit residues: 28.3251
Evaluate side-chains
  221 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 197
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -78 ASP
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -34 GLU
Chi-restraints excluded: chain A residue  -16 ILE
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
** A 293 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 = 0.3626 r_free = 0.3626 target = 0.128385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.111198 restraints weight = 13316.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114704 restraints weight = 6775.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.117105 restraints weight = 4193.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.118704 restraints weight = 2936.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.119662 restraints weight = 2250.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.4827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   8418  Z= 0.261
  Angle     :  0.714  12.826  11454  Z= 0.362
  Chirality :  0.047   0.272   1296
  Planarity :  0.005   0.054   1435
  Dihedral  :  4.754  19.372   1153
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.81 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -0.14 (0.28), residues: 1045
  helix:  1.30 (0.27), residues: 386
  sheet: -0.30 (0.34), residues: 258
  loop : -1.30 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 253 
 TYR   0.024   0.002   TYR L  50 
 PHE   0.019   0.002   PHE H 114 
 TRP   0.036   0.002   TRP A -76 
 HIS   0.004   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 8413)
  covalent geometry    : angle       0.71226 (11444)
  SS BOND              : bond        0.00379 (    5)
  SS BOND              : angle       1.67680 (   10)
  hydrogen bonds       : bond        0.04873 (  414)
  hydrogen bonds       : angle       4.97989 ( 1233)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8275 (mtpp) cc_final: 0.7990 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6595 (t0) cc_final: 0.6024 (t0)
REVERT: A  -51 LYS cc_start: 0.8272 (tttt) cc_final: 0.7808 (mttm)
REVERT: A   27 HIS cc_start: 0.5328 (OUTLIER) cc_final: 0.5107 (m-70)
REVERT: A   77 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7083 (mp)
REVERT: A  112 LEU cc_start: 0.7867 (mt) cc_final: 0.7485 (pp)
REVERT: A  115 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8286 (p)
REVERT: A  133 ARG cc_start: 0.7614 (mmt180) cc_final: 0.7272 (mmm160)
REVERT: A  144 VAL cc_start: 0.7771 (t) cc_final: 0.7555 (p)
REVERT: A  148 ARG cc_start: 0.6948 (mmm-85) cc_final: 0.6679 (mmm-85)
REVERT: A  149 TYR cc_start: 0.6568 (t80) cc_final: 0.6279 (t80)
REVERT: A  152 VAL cc_start: 0.8226 (t) cc_final: 0.7975 (p)
REVERT: A  162 LEU cc_start: 0.8085 (tp) cc_final: 0.7766 (tp)
REVERT: A  203 LEU cc_start: 0.7552 (mt) cc_final: 0.6997 (mt)
REVERT: A  283 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7593 (tp)
REVERT: A  310 ASP cc_start: 0.7237 (t0) cc_final: 0.6948 (t0)
REVERT: A  339 ILE cc_start: 0.8020 (mt) cc_final: 0.7695 (mt)
REVERT: A  373 ARG cc_start: 0.7508 (mmm160) cc_final: 0.7281 (mtp85)
REVERT: A  393 LYS cc_start: 0.7921 (mttt) cc_final: 0.7691 (mmtt)
REVERT: A  404 THR cc_start: 0.8306 (m) cc_final: 0.7957 (p)
REVERT: A  408 THR cc_start: 0.8460 (m) cc_final: 0.8188 (t)
REVERT: A  409 ILE cc_start: 0.8111 (mt) cc_final: 0.7713 (mt)
REVERT: A  411 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7688 (ttpt)
REVERT: A  412 THR cc_start: 0.8633 (m) cc_final: 0.8332 (t)
REVERT: A  434 LEU cc_start: 0.8172 (tp) cc_final: 0.7947 (tp)
REVERT: H   24 SER cc_start: 0.8579 (m) cc_final: 0.8148 (t)
REVERT: H   74 SER cc_start: 0.7968 (t) cc_final: 0.7631 (p)
REVERT: H  124 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7550 (p)
REVERT: H  131 LYS cc_start: 0.8585 (ptmm) cc_final: 0.8060 (ttpp)
REVERT: H  195 VAL cc_start: 0.8208 (p) cc_final: 0.7804 (m)
REVERT: N   83 MET cc_start: 0.6094 (ttm) cc_final: 0.5730 (ttm)
REVERT: N   89 GLU cc_start: 0.6790 (mp0) cc_final: 0.6318 (mp0)
REVERT: L   37 TYR cc_start: 0.8766 (m-10) cc_final: 0.8390 (m-80)
REVERT: L   46 LYS cc_start: 0.7997 (mttm) cc_final: 0.7683 (mttm)
  outliers start: 28
  outliers final: 21
  residues processed: 211
  average time/residue: 0.1008
  time to fit residues: 28.7886
Evaluate side-chains
  217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 191
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -78 ASP
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -34 GLU
Chi-restraints excluded: chain A residue  -16 ILE
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  119 GLN
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 79 optimal weight:    0.2980
   chunk 73 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 94 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 54 optimal weight:    0.3980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.132993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.116102 restraints weight = 13273.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.119700 restraints weight = 6777.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.122021 restraints weight = 4181.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.123666 restraints weight = 2932.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.124771 restraints weight = 2225.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.4786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8418  Z= 0.179
  Angle     :  0.674  12.533  11454  Z= 0.336
  Chirality :  0.045   0.263   1296
  Planarity :  0.004   0.046   1435
  Dihedral  :  4.592  18.609   1153
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.37 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 aren not related in a simple way.
  whole: -0.06 (0.28), residues: 1045
  helix:  1.33 (0.26), residues: 387
  sheet: -0.18 (0.35), residues: 256
  loop : -1.27 (0.34), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 253 
 TYR   0.026   0.002   TYR L  50 
 PHE   0.015   0.001   PHE H 114 
 TRP   0.035   0.002   TRP A -76 
 HIS   0.004   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8413)
  covalent geometry    : angle       0.67325 (11444)
  SS BOND              : bond        0.00266 (    5)
  SS BOND              : angle       1.38415 (   10)
  hydrogen bonds       : bond        0.04380 (  414)
  hydrogen bonds       : angle       4.79842 ( 1233)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1510.37 seconds
wall clock time: 26 minutes 53.75 seconds (1613.75 seconds total)