Starting phenix.real_space_refine
on Fri Jun  6 21:41:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hii_34817/06_2025/8hii_34817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hii_34817/06_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_34817/06_2025/8hii_34817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hii_34817/06_2025/8hii_34817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hii_34817/06_2025/8hii_34817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hii_34817/06_2025/8hii_34817.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.37, per 1000 atoms: 0.78
  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: 2.65
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.73
  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: 3.92

  Time building geometry restraints manager: 2.42 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:             94.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     29.750
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  128.340
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.037   0.002   TRP H 102 
 HIS   0.008   0.002   HIS H  38 
 PHE   0.028   0.002   PHE A 103 
 TYR   0.026   0.002   TYR A  74 
 ARG   0.004   0.000   ARG L  62 

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

*********************** 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  : 1.000 
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: 0.2336
  time to fit residues: 76.9398
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  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 94 optimal weight:    0.2980
   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 -42 GLN
A   5 GLN
A 293 ASN
A 386 GLN
A 431 GLN
H  42 GLN
H 169 ASN
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 = 0.3807 r_free = 0.3807 target = 0.140545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.122827 restraints weight = 13050.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.126614 restraints weight = 6631.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.129181 restraints weight = 4059.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8418  Z= 0.195
  Angle     :  0.607   6.056  11454  Z= 0.319
  Chirality :  0.043   0.164   1296
  Planarity :  0.004   0.038   1435
  Dihedral  :  4.640  19.867   1153
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  8.06 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.25), residues: 1045
  helix: -0.04 (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
 TRP   0.033   0.002   TRP H 102 
 HIS   0.006   0.002   HIS A 289 
 PHE   0.014   0.002   PHE A 103 
 TYR   0.020   0.002   TYR L  50 
 ARG   0.002   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  414)
  hydrogen bonds       : angle       4.96585 ( 1233)
  SS BOND              : bond        0.00322 (    5)
  SS BOND              : angle       1.46364 (   10)
  covalent geometry    : bond        0.00420 ( 8413)
  covalent geometry    : angle       0.60527 (11444)

*********************** 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
  242 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 220
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7998 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8150 (tttt) cc_final: 0.7716 (mttm)
REVERT: A  -35 LEU cc_start: 0.7393 (tt) cc_final: 0.7183 (tt)
REVERT: A  -26 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7057 (mt-10)
REVERT: A  -24 LYS cc_start: 0.7740 (mttt) cc_final: 0.7486 (mttp)
REVERT: A   42 ARG cc_start: 0.6278 (mtm110) cc_final: 0.6021 (mtm-85)
REVERT: A   79 VAL cc_start: 0.7982 (m) cc_final: 0.7773 (t)
REVERT: A   84 PHE cc_start: 0.7779 (t80) cc_final: 0.7569 (t80)
REVERT: A   88 ASP cc_start: 0.6639 (m-30) cc_final: 0.6314 (m-30)
REVERT: A   95 VAL cc_start: 0.7768 (p) cc_final: 0.7512 (t)
REVERT: A  126 TYR cc_start: 0.7828 (t80) cc_final: 0.7542 (t80)
REVERT: A  133 ARG cc_start: 0.7563 (mmt180) cc_final: 0.7264 (mmm160)
REVERT: A  162 LEU cc_start: 0.7875 (tp) cc_final: 0.7600 (tp)
REVERT: A  290 ILE cc_start: 0.8083 (mt) cc_final: 0.7768 (tt)
REVERT: A  310 ASP cc_start: 0.6840 (t0) cc_final: 0.6491 (m-30)
REVERT: A  346 GLN cc_start: 0.7789 (mt0) cc_final: 0.7544 (tt0)
REVERT: A  353 LEU cc_start: 0.7893 (mt) cc_final: 0.7689 (tp)
REVERT: A  361 SER cc_start: 0.7564 (m) cc_final: 0.7339 (p)
REVERT: A  393 LYS cc_start: 0.8382 (mttt) cc_final: 0.8179 (mttt)
REVERT: A  404 THR cc_start: 0.8436 (m) cc_final: 0.8040 (p)
REVERT: A  408 THR cc_start: 0.8404 (m) cc_final: 0.7950 (t)
REVERT: A  434 LEU cc_start: 0.8107 (tp) cc_final: 0.7884 (tp)
REVERT: H   24 SER cc_start: 0.8317 (m) cc_final: 0.7788 (t)
REVERT: H   74 SER cc_start: 0.7680 (t) cc_final: 0.7254 (p)
REVERT: H  116 TYR cc_start: 0.7937 (m-10) cc_final: 0.7727 (m-80)
REVERT: H  130 THR cc_start: 0.8202 (p) cc_final: 0.7984 (t)
REVERT: H  177 VAL cc_start: 0.8416 (t) cc_final: 0.8151 (p)
REVERT: N   83 MET cc_start: 0.6037 (ttm) cc_final: 0.5675 (ttm)
REVERT: N   89 GLU cc_start: 0.6794 (mp0) cc_final: 0.6321 (mp0)
REVERT: N   95 TYR cc_start: 0.7818 (m-10) cc_final: 0.7596 (m-80)
REVERT: L   43 LYS cc_start: 0.8834 (mttt) cc_final: 0.8535 (mtmm)
REVERT: L   46 LYS cc_start: 0.8056 (mttm) cc_final: 0.7738 (mttm)
  outliers start: 22
  outliers final: 9
  residues processed: 230
  average time/residue: 0.2406
  time to fit residues: 74.8393
Evaluate side-chains
  216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 207
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
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 88 optimal weight:    0.0370
   chunk 79 optimal weight:    0.0020
   chunk 74 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 75 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.3466

-------------------------------------------------------------------------------
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
** L 157 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 = 0.3791 r_free = 0.3791 target = 0.139421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.121976 restraints weight = 13183.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125786 restraints weight = 6669.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.128226 restraints weight = 4055.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8418  Z= 0.137
  Angle     :  0.573   6.645  11454  Z= 0.292
  Chirality :  0.042   0.130   1296
  Planarity :  0.003   0.030   1435
  Dihedral  :  4.443  17.792   1153
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.97 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.26), residues: 1045
  helix:  0.74 (0.27), residues: 386
  sheet: -0.76 (0.33), residues: 245
  loop : -1.85 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP H 102 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.011   0.001   PHE A -18 
 TYR   0.014   0.001   TYR A  22 
 ARG   0.002   0.000   ARG L  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  414)
  hydrogen bonds       : angle       4.69636 ( 1233)
  SS BOND              : bond        0.00223 (    5)
  SS BOND              : angle       1.29417 (   10)
  covalent geometry    : bond        0.00295 ( 8413)
  covalent geometry    : angle       0.57155 (11444)

*********************** 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
  228 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 208
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7961 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8135 (tttt) cc_final: 0.7650 (mttm)
REVERT: A  -26 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7029 (mt-10)
REVERT: A  -24 LYS cc_start: 0.7694 (mttt) cc_final: 0.7409 (mttp)
REVERT: A   61 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7832 (ttp-110)
REVERT: A   79 VAL cc_start: 0.8002 (m) cc_final: 0.7758 (t)
REVERT: A   95 VAL cc_start: 0.7715 (p) cc_final: 0.7456 (t)
REVERT: A  126 TYR cc_start: 0.7831 (t80) cc_final: 0.7532 (t80)
REVERT: A  133 ARG cc_start: 0.7521 (mmt180) cc_final: 0.7216 (mmm160)
REVERT: A  148 ARG cc_start: 0.6633 (mmm-85) cc_final: 0.6337 (mmm-85)
REVERT: A  162 LEU cc_start: 0.7858 (tp) cc_final: 0.7590 (tp)
REVERT: A  346 GLN cc_start: 0.7698 (mt0) cc_final: 0.7413 (tt0)
REVERT: A  361 SER cc_start: 0.7733 (m) cc_final: 0.7395 (p)
REVERT: A  393 LYS cc_start: 0.8358 (mttt) cc_final: 0.8147 (mttt)
REVERT: A  404 THR cc_start: 0.8336 (m) cc_final: 0.7794 (p)
REVERT: A  408 THR cc_start: 0.8380 (m) cc_final: 0.7856 (p)
REVERT: A  434 LEU cc_start: 0.8095 (tp) cc_final: 0.7860 (tp)
REVERT: H   10 SER cc_start: 0.7919 (p) cc_final: 0.7718 (p)
REVERT: H   24 SER cc_start: 0.8453 (m) cc_final: 0.7985 (t)
REVERT: H   74 SER cc_start: 0.7750 (t) cc_final: 0.7324 (p)
REVERT: H  114 PHE cc_start: 0.8053 (m-80) cc_final: 0.7849 (m-10)
REVERT: H  116 TYR cc_start: 0.7943 (m-10) cc_final: 0.7720 (m-80)
REVERT: H  152 LEU cc_start: 0.7672 (tp) cc_final: 0.7436 (tp)
REVERT: H  177 VAL cc_start: 0.8403 (t) cc_final: 0.8137 (p)
REVERT: N   89 GLU cc_start: 0.6736 (mp0) cc_final: 0.6256 (mp0)
REVERT: L   43 LYS cc_start: 0.8820 (mttt) cc_final: 0.8529 (mtmm)
REVERT: L   46 LYS cc_start: 0.8029 (mttm) cc_final: 0.7700 (mttm)
REVERT: L  111 THR cc_start: 0.8629 (p) cc_final: 0.8418 (p)
  outliers start: 20
  outliers final: 12
  residues processed: 214
  average time/residue: 0.2149
  time to fit residues: 61.3894
Evaluate side-chains
  214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 202
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
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   98 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  203 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   59 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 88 optimal weight:    0.3980
   chunk 3 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A -12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 191 HIS
L 212 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.119383 restraints weight = 13209.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.123134 restraints weight = 6699.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125574 restraints weight = 4105.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8418  Z= 0.200
  Angle     :  0.628   9.483  11454  Z= 0.322
  Chirality :  0.044   0.235   1296
  Planarity :  0.004   0.043   1435
  Dihedral  :  4.578  19.569   1153
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.33 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.27), residues: 1045
  helix:  1.02 (0.27), residues: 383
  sheet: -0.61 (0.34), residues: 245
  loop : -1.70 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  25 
 HIS   0.007   0.002   HIS L 191 
 PHE   0.015   0.001   PHE L 141 
 TYR   0.012   0.002   TYR A  31 
 ARG   0.010   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  414)
  hydrogen bonds       : angle       4.84018 ( 1233)
  SS BOND              : bond        0.00336 (    5)
  SS BOND              : angle       1.53810 (   10)
  covalent geometry    : bond        0.00437 ( 8413)
  covalent geometry    : angle       0.62654 (11444)

*********************** 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
  220 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7919 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8198 (tttt) cc_final: 0.7740 (mtmt)
REVERT: A  -26 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6952 (mt-10)
REVERT: A  -24 LYS cc_start: 0.7843 (mttt) cc_final: 0.7479 (mttp)
REVERT: A  -15 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7955 (tp)
REVERT: A   77 LEU cc_start: 0.7425 (mt) cc_final: 0.7210 (mt)
REVERT: A   79 VAL cc_start: 0.8031 (m) cc_final: 0.7705 (t)
REVERT: A   95 VAL cc_start: 0.7749 (p) cc_final: 0.7523 (t)
REVERT: A  133 ARG cc_start: 0.7583 (mmt180) cc_final: 0.7290 (mmm160)
REVERT: A  148 ARG cc_start: 0.6812 (mmm-85) cc_final: 0.6443 (mmm-85)
REVERT: A  162 LEU cc_start: 0.7997 (tp) cc_final: 0.7686 (tp)
REVERT: A  204 LYS cc_start: 0.8483 (tttt) cc_final: 0.8253 (tttt)
REVERT: A  310 ASP cc_start: 0.7294 (t0) cc_final: 0.6879 (t0)
REVERT: A  346 GLN cc_start: 0.7685 (mt0) cc_final: 0.7366 (tt0)
REVERT: A  361 SER cc_start: 0.7771 (m) cc_final: 0.7398 (p)
REVERT: A  393 LYS cc_start: 0.8327 (mttt) cc_final: 0.8047 (mttt)
REVERT: A  404 THR cc_start: 0.8333 (m) cc_final: 0.7908 (p)
REVERT: A  408 THR cc_start: 0.8527 (m) cc_final: 0.8071 (t)
REVERT: A  409 ILE cc_start: 0.7943 (mt) cc_final: 0.7658 (mt)
REVERT: A  411 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7746 (ttpt)
REVERT: A  434 LEU cc_start: 0.8133 (tp) cc_final: 0.7873 (tp)
REVERT: H   24 SER cc_start: 0.8514 (m) cc_final: 0.7984 (t)
REVERT: H   74 SER cc_start: 0.7872 (t) cc_final: 0.7529 (p)
REVERT: H  152 LEU cc_start: 0.7752 (tp) cc_final: 0.7507 (tp)
REVERT: N   89 GLU cc_start: 0.6670 (mp0) cc_final: 0.6195 (mp0)
REVERT: L    6 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8007 (p)
REVERT: L   46 LYS cc_start: 0.8093 (mttm) cc_final: 0.7737 (mttm)
  outliers start: 24
  outliers final: 15
  residues processed: 208
  average time/residue: 0.2275
  time to fit residues: 64.1276
Evaluate side-chains
  213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  -15 LEU
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  283 LEU
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain L residue    6 THR
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 81 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0870
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
A -12 GLN
A 120 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.119597 restraints weight = 13001.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.123367 restraints weight = 6671.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125661 restraints weight = 4102.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8418  Z= 0.172
  Angle     :  0.607   8.217  11454  Z= 0.309
  Chirality :  0.043   0.245   1296
  Planarity :  0.004   0.036   1435
  Dihedral  :  4.470  18.490   1153
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.68 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.27), residues: 1045
  helix:  1.20 (0.27), residues: 386
  sheet: -0.43 (0.34), residues: 245
  loop : -1.57 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  25 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.022   0.001   PHE H 114 
 TYR   0.012   0.002   TYR A 149 
 ARG   0.012   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  414)
  hydrogen bonds       : angle       4.75118 ( 1233)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       1.40177 (   10)
  covalent geometry    : bond        0.00376 ( 8413)
  covalent geometry    : angle       0.60551 (11444)

*********************** 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
  213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -68 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7925 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8262 (tttt) cc_final: 0.7742 (mttm)
REVERT: A  -26 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6969 (mt-10)
REVERT: A  -25 MET cc_start: 0.7197 (ttt) cc_final: 0.6712 (ttp)
REVERT: A  -24 LYS cc_start: 0.7826 (mttt) cc_final: 0.7477 (mttp)
REVERT: A   41 ILE cc_start: 0.7635 (mt) cc_final: 0.7409 (tt)
REVERT: A   77 LEU cc_start: 0.7432 (mt) cc_final: 0.7169 (mt)
REVERT: A   95 VAL cc_start: 0.7755 (p) cc_final: 0.7546 (t)
REVERT: A  133 ARG cc_start: 0.7559 (mmt180) cc_final: 0.7264 (mmm160)
REVERT: A  152 VAL cc_start: 0.8157 (t) cc_final: 0.7763 (p)
REVERT: A  162 LEU cc_start: 0.8026 (tp) cc_final: 0.7699 (tp)
REVERT: A  204 LYS cc_start: 0.8483 (tttt) cc_final: 0.8278 (tttt)
REVERT: A  310 ASP cc_start: 0.7225 (t0) cc_final: 0.6858 (t0)
REVERT: A  346 GLN cc_start: 0.7668 (mt0) cc_final: 0.7315 (tt0)
REVERT: A  361 SER cc_start: 0.7732 (m) cc_final: 0.7352 (p)
REVERT: A  373 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7422 (mmm-85)
REVERT: A  393 LYS cc_start: 0.8354 (mttt) cc_final: 0.8053 (mttt)
REVERT: A  404 THR cc_start: 0.8273 (m) cc_final: 0.7754 (p)
REVERT: A  408 THR cc_start: 0.8497 (m) cc_final: 0.8006 (p)
REVERT: A  409 ILE cc_start: 0.7990 (mt) cc_final: 0.7683 (mt)
REVERT: A  411 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7630 (ttpt)
REVERT: A  434 LEU cc_start: 0.8142 (tp) cc_final: 0.7922 (tp)
REVERT: H   24 SER cc_start: 0.8558 (m) cc_final: 0.8062 (t)
REVERT: H   74 SER cc_start: 0.7929 (t) cc_final: 0.7578 (p)
REVERT: H  195 VAL cc_start: 0.8115 (p) cc_final: 0.7721 (m)
REVERT: N   89 GLU cc_start: 0.6706 (mp0) cc_final: 0.6222 (mp0)
REVERT: L   46 LYS cc_start: 0.8122 (mttm) cc_final: 0.7773 (mttm)
  outliers start: 21
  outliers final: 16
  residues processed: 200
  average time/residue: 0.2370
  time to fit residues: 63.7465
Evaluate side-chains
  207 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 191
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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  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 N residue   86 LEU
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  104 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 82 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A -12 GLN
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.135521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.118325 restraints weight = 13194.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.122082 restraints weight = 6685.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.124421 restraints weight = 4074.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.4084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8418  Z= 0.194
  Angle     :  0.623  10.306  11454  Z= 0.317
  Chirality :  0.044   0.257   1296
  Planarity :  0.004   0.038   1435
  Dihedral  :  4.479  19.098   1153
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.01 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 1045
  helix:  1.26 (0.27), residues: 386
  sheet: -0.37 (0.34), residues: 243
  loop : -1.51 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  25 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.027   0.001   PHE A  84 
 TYR   0.011   0.002   TYR L 142 
 ARG   0.009   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  414)
  hydrogen bonds       : angle       4.79593 ( 1233)
  SS BOND              : bond        0.00302 (    5)
  SS BOND              : angle       1.48783 (   10)
  covalent geometry    : bond        0.00424 ( 8413)
  covalent geometry    : angle       0.62154 (11444)

*********************** 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
  227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.8293 (tt) cc_final: 0.8008 (tt)
REVERT: A  -68 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7940 (mtpp)
REVERT: A  -51 LYS cc_start: 0.8297 (tttt) cc_final: 0.7759 (mttm)
REVERT: A  -49 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7414 (ttm-80)
REVERT: A  -26 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7002 (mt-10)
REVERT: A  -25 MET cc_start: 0.7359 (ttt) cc_final: 0.6901 (ttp)
REVERT: A  -24 LYS cc_start: 0.7858 (mttt) cc_final: 0.7508 (mttp)
REVERT: A   27 HIS cc_start: 0.5615 (OUTLIER) cc_final: 0.4924 (m-70)
REVERT: A   61 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7969 (ttp-110)
REVERT: A   77 LEU cc_start: 0.7558 (mt) cc_final: 0.7320 (mt)
REVERT: A  115 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8149 (p)
REVERT: A  152 VAL cc_start: 0.8125 (t) cc_final: 0.7790 (p)
REVERT: A  162 LEU cc_start: 0.8044 (tp) cc_final: 0.7726 (tp)
REVERT: A  203 LEU cc_start: 0.7367 (mt) cc_final: 0.6839 (mt)
REVERT: A  310 ASP cc_start: 0.7259 (t0) cc_final: 0.6888 (t0)
REVERT: A  393 LYS cc_start: 0.8289 (mttt) cc_final: 0.7939 (mttt)
REVERT: A  404 THR cc_start: 0.8284 (m) cc_final: 0.7761 (p)
REVERT: A  408 THR cc_start: 0.8451 (m) cc_final: 0.7982 (p)
REVERT: A  409 ILE cc_start: 0.8043 (mt) cc_final: 0.7688 (mt)
REVERT: A  411 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7627 (ttpt)
REVERT: A  434 LEU cc_start: 0.8141 (tp) cc_final: 0.7912 (tp)
REVERT: H   24 SER cc_start: 0.8566 (m) cc_final: 0.8076 (t)
REVERT: H   74 SER cc_start: 0.7950 (t) cc_final: 0.7603 (p)
REVERT: H  195 VAL cc_start: 0.8152 (p) cc_final: 0.7741 (m)
REVERT: N   89 GLU cc_start: 0.6720 (mp0) cc_final: 0.6212 (mp0)
REVERT: L    6 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8033 (p)
REVERT: L   37 TYR cc_start: 0.8803 (m-10) cc_final: 0.8378 (m-80)
REVERT: L   46 LYS cc_start: 0.8132 (mttm) cc_final: 0.7773 (mttm)
REVERT: L  160 ASN cc_start: 0.8086 (p0) cc_final: 0.7862 (p0)
  outliers start: 28
  outliers final: 15
  residues processed: 214
  average time/residue: 0.2475
  time to fit residues: 69.8099
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  : 0.822 
-------------------------------------------------------------------------------
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   23 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    6 THR
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   99 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 16 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.133750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.116558 restraints weight = 13148.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.120309 restraints weight = 6592.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.122745 restraints weight = 3999.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8418  Z= 0.201
  Angle     :  0.644  11.563  11454  Z= 0.326
  Chirality :  0.045   0.269   1296
  Planarity :  0.004   0.052   1435
  Dihedral  :  4.515  19.173   1153
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.36 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.27), residues: 1045
  helix:  1.30 (0.27), residues: 384
  sheet: -0.26 (0.35), residues: 243
  loop : -1.46 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  25 
 HIS   0.003   0.001   HIS A 289 
 PHE   0.019   0.001   PHE H 114 
 TYR   0.029   0.002   TYR L  50 
 ARG   0.010   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04403 (  414)
  hydrogen bonds       : angle       4.78838 ( 1233)
  SS BOND              : bond        0.00316 (    5)
  SS BOND              : angle       1.47578 (   10)
  covalent geometry    : bond        0.00440 ( 8413)
  covalent geometry    : angle       0.64236 (11444)

*********************** 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: 25
    poor density    : 197
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.8287 (tt) cc_final: 0.8034 (tt)
REVERT: A  -68 LYS cc_start: 0.8287 (mtpp) cc_final: 0.7990 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6540 (t0) cc_final: 0.5925 (t0)
REVERT: A  -51 LYS cc_start: 0.8272 (tttt) cc_final: 0.7704 (mttm)
REVERT: A  -49 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7398 (tpt-90)
REVERT: A  -24 LYS cc_start: 0.7847 (mttt) cc_final: 0.7475 (mttp)
REVERT: A   27 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.5204 (m-70)
REVERT: A   61 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7937 (ttp-110)
REVERT: A  112 LEU cc_start: 0.7854 (mt) cc_final: 0.7383 (pp)
REVERT: A  141 PHE cc_start: 0.7600 (t80) cc_final: 0.7232 (t80)
REVERT: A  152 VAL cc_start: 0.8224 (t) cc_final: 0.7908 (p)
REVERT: A  162 LEU cc_start: 0.8043 (tp) cc_final: 0.7718 (tp)
REVERT: A  203 LEU cc_start: 0.7499 (mt) cc_final: 0.6858 (tp)
REVERT: A  310 ASP cc_start: 0.7271 (t0) cc_final: 0.6925 (t0)
REVERT: A  339 ILE cc_start: 0.7788 (mt) cc_final: 0.7449 (mt)
REVERT: A  373 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7455 (mmm-85)
REVERT: A  393 LYS cc_start: 0.8240 (mttt) cc_final: 0.7963 (mttt)
REVERT: A  404 THR cc_start: 0.8286 (m) cc_final: 0.7786 (p)
REVERT: A  408 THR cc_start: 0.8517 (m) cc_final: 0.7951 (p)
REVERT: A  409 ILE cc_start: 0.8040 (mt) cc_final: 0.7696 (mt)
REVERT: A  434 LEU cc_start: 0.8139 (tp) cc_final: 0.7904 (tp)
REVERT: H   24 SER cc_start: 0.8571 (m) cc_final: 0.8097 (t)
REVERT: H   74 SER cc_start: 0.7904 (t) cc_final: 0.7580 (p)
REVERT: H  195 VAL cc_start: 0.8139 (p) cc_final: 0.7752 (m)
REVERT: N   89 GLU cc_start: 0.6788 (mp0) cc_final: 0.6228 (mp0)
REVERT: L    6 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8022 (p)
REVERT: L   37 TYR cc_start: 0.8768 (m-10) cc_final: 0.8357 (m-80)
REVERT: L   46 LYS cc_start: 0.8113 (mttm) cc_final: 0.7742 (mttm)
REVERT: L  123 SER cc_start: 0.8108 (p) cc_final: 0.7889 (t)
  outliers start: 25
  outliers final: 17
  residues processed: 211
  average time/residue: 0.2073
  time to fit residues: 58.7369
Evaluate side-chains
  211 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 192
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  134 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain H residue   23 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    6 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  165 VAL
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 39 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   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 -12 GLN
A 277 ASN
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.129081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.111867 restraints weight = 13261.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.115430 restraints weight = 6737.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117834 restraints weight = 4137.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.4586

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= 0.240
  Angle     :  0.673   9.559  11454  Z= 0.344
  Chirality :  0.046   0.266   1296
  Planarity :  0.004   0.044   1435
  Dihedral  :  4.678  20.334   1153
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.47 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.27), residues: 1045
  helix:  1.32 (0.26), residues: 385
  sheet: -0.14 (0.35), residues: 238
  loop : -1.41 (0.33), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  25 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.019   0.001   PHE A  84 
 TYR   0.028   0.002   TYR L  50 
 ARG   0.011   0.001   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04729 (  414)
  hydrogen bonds       : angle       4.92378 ( 1233)
  SS BOND              : bond        0.00371 (    5)
  SS BOND              : angle       1.52989 (   10)
  covalent geometry    : bond        0.00524 ( 8413)
  covalent geometry    : angle       0.67167 (11444)

*********************** 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
  226 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.8278 (tt) cc_final: 0.8065 (tt)
REVERT: A  -68 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8048 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6615 (t0) cc_final: 0.5994 (t0)
REVERT: A  -51 LYS cc_start: 0.8259 (tttt) cc_final: 0.7781 (mttm)
REVERT: A  -25 MET cc_start: 0.7432 (ttt) cc_final: 0.7019 (ttp)
REVERT: A   27 HIS cc_start: 0.5437 (OUTLIER) cc_final: 0.5084 (m-70)
REVERT: A   61 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8009 (ttp-110)
REVERT: A  112 LEU cc_start: 0.7885 (mt) cc_final: 0.7446 (pp)
REVERT: A  115 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (p)
REVERT: A  141 PHE cc_start: 0.7564 (t80) cc_final: 0.7214 (t80)
REVERT: A  144 VAL cc_start: 0.7825 (t) cc_final: 0.7577 (p)
REVERT: A  152 VAL cc_start: 0.8276 (t) cc_final: 0.7988 (p)
REVERT: A  162 LEU cc_start: 0.8090 (tp) cc_final: 0.7765 (tp)
REVERT: A  173 LEU cc_start: 0.7694 (mt) cc_final: 0.7345 (mt)
REVERT: A  203 LEU cc_start: 0.7561 (mt) cc_final: 0.6913 (tp)
REVERT: A  310 ASP cc_start: 0.7246 (t0) cc_final: 0.6983 (t0)
REVERT: A  339 ILE cc_start: 0.7989 (mt) cc_final: 0.7644 (mt)
REVERT: A  373 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7388 (mmm-85)
REVERT: A  393 LYS cc_start: 0.8270 (mttt) cc_final: 0.8020 (mttt)
REVERT: A  404 THR cc_start: 0.8336 (m) cc_final: 0.7782 (p)
REVERT: A  408 THR cc_start: 0.8453 (m) cc_final: 0.7993 (p)
REVERT: A  409 ILE cc_start: 0.8039 (mt) cc_final: 0.7738 (mt)
REVERT: A  411 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7668 (ttpt)
REVERT: A  434 LEU cc_start: 0.8185 (tp) cc_final: 0.7940 (tp)
REVERT: H   24 SER cc_start: 0.8583 (m) cc_final: 0.8168 (t)
REVERT: H   74 SER cc_start: 0.7946 (t) cc_final: 0.7607 (p)
REVERT: H  195 VAL cc_start: 0.8202 (p) cc_final: 0.7779 (m)
REVERT: N   89 GLU cc_start: 0.6794 (mp0) cc_final: 0.6251 (mp0)
REVERT: L    6 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8030 (p)
REVERT: L   34 VAL cc_start: 0.8426 (t) cc_final: 0.7983 (p)
REVERT: L   37 TYR cc_start: 0.8777 (m-10) cc_final: 0.8376 (m-80)
REVERT: L   46 LYS cc_start: 0.8061 (mttm) cc_final: 0.7682 (mttm)
  outliers start: 27
  outliers final: 19
  residues processed: 213
  average time/residue: 0.2130
  time to fit residues: 61.2341
Evaluate side-chains
  218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  173 LEU
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  165 VAL
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 88 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0040
   chunk 96 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 100 optimal weight:    0.1980
   chunk 78 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.3792

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
** 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 = 0.3704 r_free = 0.3704 target = 0.133724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.116368 restraints weight = 13330.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.120188 restraints weight = 6662.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.122514 restraints weight = 4026.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.4558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8418  Z= 0.151
  Angle     :  0.648  13.309  11454  Z= 0.322
  Chirality :  0.044   0.267   1296
  Planarity :  0.004   0.044   1435
  Dihedral  :  4.482  18.850   1153
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.26 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.28), residues: 1045
  helix:  1.48 (0.26), residues: 385
  sheet: -0.19 (0.35), residues: 243
  loop : -1.29 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A -76 
 HIS   0.003   0.001   HIS A  27 
 PHE   0.016   0.001   PHE H 114 
 TYR   0.029   0.002   TYR L  50 
 ARG   0.010   0.001   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04181 (  414)
  hydrogen bonds       : angle       4.71647 ( 1233)
  SS BOND              : bond        0.00242 (    5)
  SS BOND              : angle       1.26208 (   10)
  covalent geometry    : bond        0.00333 ( 8413)
  covalent geometry    : angle       0.64748 (11444)

*********************** 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
  218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.8314 (tt) cc_final: 0.8085 (tt)
REVERT: A  -68 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8045 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6578 (t0) cc_final: 0.5959 (t0)
REVERT: A  -51 LYS cc_start: 0.8225 (tttt) cc_final: 0.7671 (mttm)
REVERT: A  -25 MET cc_start: 0.7295 (ttt) cc_final: 0.6861 (ttp)
REVERT: A    0 LYS cc_start: 0.7946 (mttm) cc_final: 0.7672 (mttp)
REVERT: A   27 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.5053 (m-70)
REVERT: A   61 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7967 (ttp80)
REVERT: A  112 LEU cc_start: 0.7822 (mt) cc_final: 0.7399 (pp)
REVERT: A  115 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8097 (p)
REVERT: A  144 VAL cc_start: 0.7768 (t) cc_final: 0.7494 (p)
REVERT: A  152 VAL cc_start: 0.8216 (t) cc_final: 0.7937 (p)
REVERT: A  162 LEU cc_start: 0.8043 (tp) cc_final: 0.7727 (tp)
REVERT: A  203 LEU cc_start: 0.7442 (mt) cc_final: 0.6894 (mt)
REVERT: A  310 ASP cc_start: 0.7272 (t0) cc_final: 0.6978 (t0)
REVERT: A  339 ILE cc_start: 0.7929 (mt) cc_final: 0.7581 (mt)
REVERT: A  373 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7423 (mmm-85)
REVERT: A  404 THR cc_start: 0.8287 (m) cc_final: 0.7891 (p)
REVERT: A  408 THR cc_start: 0.8421 (m) cc_final: 0.8170 (t)
REVERT: A  409 ILE cc_start: 0.8040 (mt) cc_final: 0.7760 (mt)
REVERT: A  411 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7737 (ttpt)
REVERT: A  434 LEU cc_start: 0.8143 (tp) cc_final: 0.7898 (tp)
REVERT: H   24 SER cc_start: 0.8509 (m) cc_final: 0.8026 (t)
REVERT: H   74 SER cc_start: 0.7948 (t) cc_final: 0.7591 (p)
REVERT: H  124 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7491 (p)
REVERT: H  195 VAL cc_start: 0.8128 (p) cc_final: 0.7752 (m)
REVERT: N   89 GLU cc_start: 0.6731 (mp0) cc_final: 0.6190 (mp0)
REVERT: L    6 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8025 (p)
REVERT: L   37 TYR cc_start: 0.8736 (m-10) cc_final: 0.8370 (m-80)
REVERT: L   46 LYS cc_start: 0.8048 (mttm) cc_final: 0.7701 (mttm)
  outliers start: 19
  outliers final: 13
  residues processed: 212
  average time/residue: 0.2062
  time to fit residues: 59.0152
Evaluate side-chains
  210 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 193
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
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  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  124 THR
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   99 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 57 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   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 -12 GLN
A 120 GLN
** 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 = 0.3686 r_free = 0.3686 target = 0.132811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.115722 restraints weight = 13090.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.119391 restraints weight = 6573.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.121877 restraints weight = 4002.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8418  Z= 0.211
  Angle     :  0.697  13.511  11454  Z= 0.347
  Chirality :  0.046   0.276   1296
  Planarity :  0.004   0.054   1435
  Dihedral  :  4.577  18.868   1153
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.70 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.27), residues: 1045
  helix:  1.40 (0.26), residues: 386
  sheet: -0.11 (0.36), residues: 232
  loop : -1.33 (0.33), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  25 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.017   0.001   PHE H 114 
 TYR   0.028   0.002   TYR L  50 
 ARG   0.010   0.001   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  414)
  hydrogen bonds       : angle       4.84469 ( 1233)
  SS BOND              : bond        0.00298 (    5)
  SS BOND              : angle       1.46236 (   10)
  covalent geometry    : bond        0.00467 ( 8413)
  covalent geometry    : angle       0.69624 (11444)

********************** 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
  214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.8330 (tt) cc_final: 0.8085 (tt)
REVERT: A  -68 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8061 (mtpp)
REVERT: A  -55 ASP cc_start: 0.6582 (t0) cc_final: 0.5909 (t0)
REVERT: A  -51 LYS cc_start: 0.8225 (tttt) cc_final: 0.7670 (mttm)
REVERT: A    0 LYS cc_start: 0.7977 (mttm) cc_final: 0.7669 (mttp)
REVERT: A   27 HIS cc_start: 0.5345 (OUTLIER) cc_final: 0.5128 (m-70)
REVERT: A   61 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.8046 (ttp-110)
REVERT: A  102 SER cc_start: 0.7754 (m) cc_final: 0.7339 (p)
REVERT: A  112 LEU cc_start: 0.7861 (mt) cc_final: 0.7422 (pp)
REVERT: A  115 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8201 (p)
REVERT: A  144 VAL cc_start: 0.7775 (t) cc_final: 0.7446 (p)
REVERT: A  152 VAL cc_start: 0.8377 (t) cc_final: 0.8100 (p)
REVERT: A  162 LEU cc_start: 0.8075 (tp) cc_final: 0.7757 (tp)
REVERT: A  173 LEU cc_start: 0.7774 (mt) cc_final: 0.7383 (mp)
REVERT: A  203 LEU cc_start: 0.7509 (mt) cc_final: 0.6913 (tp)
REVERT: A  310 ASP cc_start: 0.7246 (t0) cc_final: 0.6954 (t0)
REVERT: A  339 ILE cc_start: 0.7993 (mt) cc_final: 0.7666 (mt)
REVERT: A  373 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7361 (mmm-85)
REVERT: A  393 LYS cc_start: 0.8319 (mttt) cc_final: 0.8061 (mttt)
REVERT: A  404 THR cc_start: 0.8307 (m) cc_final: 0.7917 (p)
REVERT: A  408 THR cc_start: 0.8426 (m) cc_final: 0.8149 (t)
REVERT: A  409 ILE cc_start: 0.8059 (mt) cc_final: 0.7769 (mt)
REVERT: A  411 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7757 (ttpt)
REVERT: A  434 LEU cc_start: 0.8146 (tp) cc_final: 0.7908 (tp)
REVERT: H   24 SER cc_start: 0.8422 (m) cc_final: 0.7907 (t)
REVERT: H   74 SER cc_start: 0.7943 (t) cc_final: 0.7615 (p)
REVERT: H  124 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7501 (p)
REVERT: H  195 VAL cc_start: 0.8201 (p) cc_final: 0.7779 (m)
REVERT: N   89 GLU cc_start: 0.6742 (mp0) cc_final: 0.6204 (mp0)
REVERT: L    6 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8090 (p)
REVERT: L   37 TYR cc_start: 0.8774 (m-10) cc_final: 0.8411 (m-80)
REVERT: L   46 LYS cc_start: 0.8014 (mttm) cc_final: 0.7689 (mttm)
  outliers start: 21
  outliers final: 16
  residues processed: 206
  average time/residue: 0.2097
  time to fit residues: 58.3140
Evaluate side-chains
  213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 193
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
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  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 N residue    7 SER
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   75 THR
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:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A -12 GLN
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116176 restraints weight = 13386.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.119756 restraints weight = 6768.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.122141 restraints weight = 4151.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8418  Z= 0.200
  Angle     :  0.698  13.579  11454  Z= 0.345
  Chirality :  0.046   0.274   1296
  Planarity :  0.004   0.046   1435
  Dihedral  :  4.573  18.527   1153
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.27), residues: 1045
  helix:  1.40 (0.26), residues: 386
  sheet: -0.09 (0.36), residues: 232
  loop : -1.31 (0.33), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A -76 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.018   0.001   PHE H 114 
 TYR   0.028   0.002   TYR L  50 
 ARG   0.009   0.001   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04435 (  414)
  hydrogen bonds       : angle       4.81357 ( 1233)
  SS BOND              : bond        0.00325 (    5)
  SS BOND              : angle       1.43781 (   10)
  covalent geometry    : bond        0.00447 ( 8413)
  covalent geometry    : angle       0.69739 (11444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3409.91 seconds
wall clock time: 61 minutes 29.59 seconds (3689.59 seconds total)