Starting phenix.real_space_refine
on Thu Jun  5 06:47:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gh4_51346/06_2025/9gh4_51346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gh4_51346/06_2025/9gh4_51346.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gh4_51346/06_2025/9gh4_51346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gh4_51346/06_2025/9gh4_51346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gh4_51346/06_2025/9gh4_51346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gh4_51346/06_2025/9gh4_51346.cif"
  }
  resolution = 3.8
  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=   0.000 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       6      5.16       5
     C    3333      2.51       5
     N     978      2.21       5
     O    1137      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5454
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1818
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 1, 'TRANS': 248}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 3.79, per 1000 atoms: 0.69
  Number of scatterers: 5454
  At special positions: 0
  Unit cell: (60.59, 58.93, 137.78, 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       6     16.00
     O    1137      8.00
     N     978      7.00
     C    3333      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.31
  Conformation dependent library (CDL) restraints added in 779.7 milliseconds
  

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1302

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      11.2% alpha, 32.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 231 through 238
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 254 through 261
      removed outlier: 3.644A  pdb=" N   TYR A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.616A  pdb=" N   LYS A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 238
    Processing helix  chain 'B' and resid 245 through 250
    Processing helix  chain 'B' and resid 254 through 261
      removed outlier: 3.644A  pdb=" N   TYR B 258 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 273
      removed outlier: 3.617A  pdb=" N   LYS B 272 " --> pdb=" O   LYS B 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 238
    Processing helix  chain 'C' and resid 245 through 250
    Processing helix  chain 'C' and resid 254 through 261
      removed outlier: 3.644A  pdb=" N   TYR C 258 " --> pdb=" O   ARG C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 273
      removed outlier: 3.616A  pdb=" N   LYS C 272 " --> pdb=" O   LYS C 268 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 6.827A  pdb=" N   SER A  66 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLY A  83 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE A  68 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   SER A  94 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY A 111 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   PHE A  96 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LYS A 113 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   SER A  98 " --> pdb=" O   LYS A 113 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   THR A 115 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN A 114 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN A 129 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 129 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   ASN A 151 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLN A 129 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.802A  pdb=" N   VAL A  45 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LYS A  59 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG A  73 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ILE A  87 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA A 101 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN A 114 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN A 129 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 129 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR A 157 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL A 189 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165
      removed outlier: 6.773A  pdb=" N   LYS A 164 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 215
      removed outlier: 6.114A  pdb=" N   LYS A 213 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL C 189 " --> pdb=" O   SER C 204 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR C 157 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASN C 114 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN C 129 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL C 116 " --> pdb=" O   GLN C 129 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ILE C  87 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG C  73 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS C  59 " --> pdb=" O   ALA C  74 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL C  45 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31
      removed outlier: 6.827A  pdb=" N   SER C  66 " --> pdb=" O   ALA C  81 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLY C  83 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE C  68 " --> pdb=" O   GLY C  83 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   SER C  94 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY C 111 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   PHE C  96 " --> pdb=" O   GLY C 111 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LYS C 113 " --> pdb=" O   PHE C  96 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   SER C  98 " --> pdb=" O   LYS C 113 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   THR C 115 " --> pdb=" O   SER C  98 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASN C 114 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN C 129 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL C 116 " --> pdb=" O   GLN C 129 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   ASN C 151 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLN C 129 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 31
      removed outlier: 6.828A  pdb=" N   SER B  66 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLY B  83 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   PHE B  68 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   SER B  94 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY B 111 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   PHE B  96 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LYS B 113 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   SER B  98 " --> pdb=" O   LYS B 113 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   THR B 115 " --> pdb=" O   SER B  98 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN B 114 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN B 129 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL B 116 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
      removed outlier: 8.741A  pdb=" N   ASN B 151 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   GLN B 129 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 46
      removed outlier: 6.801A  pdb=" N   VAL B  45 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS B  59 " --> pdb=" O   ALA B  74 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG B  73 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ILE B  87 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA B 101 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN B 114 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN B 129 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL B 116 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR B 157 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   VAL B 189 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 165
      removed outlier: 6.773A  pdb=" N   LYS B 164 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 165
      removed outlier: 6.774A  pdb=" N   LYS C 164 " --> pdb=" O   ILE C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    145 hydrogen bonds defined for protein.
    417 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.57 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: 1899
        1.34 -     1.46: 1035
        1.46 -     1.57: 2592
        1.57 -     1.69: 0
        1.69 -     1.80: 12
  Bond restraints: 5538
  Sorted by residual:
  bond pdb=" C   VAL C 205 "
       pdb=" O   VAL C 205 "
    ideal  model  delta    sigma   weight residual
    1.242  1.229  0.014 1.23e-02 6.61e+03 1.21e+00
  bond pdb=" C   VAL B 205 "
       pdb=" O   VAL B 205 "
    ideal  model  delta    sigma   weight residual
    1.242  1.229  0.013 1.23e-02 6.61e+03 1.17e+00
  bond pdb=" C   VAL A 205 "
       pdb=" O   VAL A 205 "
    ideal  model  delta    sigma   weight residual
    1.242  1.229  0.013 1.23e-02 6.61e+03 1.11e+00
  bond pdb=" CB  GLU A 142 "
       pdb=" CG  GLU A 142 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  GLU B 142 "
       pdb=" CG  GLU B 142 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.04e+00
  ... (remaining 5533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 7392
        2.09 -     4.17: 57
        4.17 -     6.26: 9
        6.26 -     8.35: 6
        8.35 -    10.44: 3
  Bond angle restraints: 7467
  Sorted by residual:
  angle pdb=" CA  LEU C 235 "
        pdb=" CB  LEU C 235 "
        pdb=" CG  LEU C 235 "
      ideal   model   delta    sigma   weight residual
     116.30  126.74  -10.44 3.50e+00 8.16e-02 8.89e+00
  angle pdb=" CA  LEU A 235 "
        pdb=" CB  LEU A 235 "
        pdb=" CG  LEU A 235 "
      ideal   model   delta    sigma   weight residual
     116.30  126.72  -10.42 3.50e+00 8.16e-02 8.86e+00
  angle pdb=" CA  LEU B 235 "
        pdb=" CB  LEU B 235 "
        pdb=" CG  LEU B 235 "
      ideal   model   delta    sigma   weight residual
     116.30  126.69  -10.39 3.50e+00 8.16e-02 8.82e+00
  angle pdb=" N   GLY C  55 "
        pdb=" CA  GLY C  55 "
        pdb=" C   GLY C  55 "
      ideal   model   delta    sigma   weight residual
     111.21  113.84   -2.63 1.04e+00 9.25e-01 6.38e+00
  angle pdb=" N   GLY A  55 "
        pdb=" CA  GLY A  55 "
        pdb=" C   GLY A  55 "
      ideal   model   delta    sigma   weight residual
     111.21  113.82   -2.61 1.04e+00 9.25e-01 6.29e+00
  ... (remaining 7462 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 2791
       17.83 -    35.66: 308
       35.66 -    53.49: 90
       53.49 -    71.32: 6
       71.32 -    89.15: 6
  Dihedral angle restraints: 3201
    sinusoidal: 1131
      harmonic: 2070
  Sorted by residual:
  dihedral pdb=" CG  LYS A  50 "
           pdb=" CD  LYS A  50 "
           pdb=" CE  LYS A  50 "
           pdb=" NZ  LYS A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.24  -59.76     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS C  50 "
           pdb=" CD  LYS C  50 "
           pdb=" CE  LYS C  50 "
           pdb=" NZ  LYS C  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.25  -59.75     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS B  50 "
           pdb=" CD  LYS B  50 "
           pdb=" CE  LYS B  50 "
           pdb=" NZ  LYS B  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.28  -59.72     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3198 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 356
       0.023 -    0.046: 211
       0.046 -    0.068: 140
       0.068 -    0.091: 31
       0.091 -    0.114: 60
  Chirality restraints: 798
  Sorted by residual:
  chirality pdb=" CA  ILE B 181 "
            pdb=" N   ILE B 181 "
            pdb=" C   ILE B 181 "
            pdb=" CB  ILE B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.26e-01
  chirality pdb=" CA  ILE C 159 "
            pdb=" N   ILE C 159 "
            pdb=" C   ILE C 159 "
            pdb=" CB  ILE C 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.24e-01
  chirality pdb=" CA  ILE A 159 "
            pdb=" N   ILE A 159 "
            pdb=" C   ILE A 159 "
            pdb=" CB  ILE A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 795 not shown)

  Planarity restraints: 1014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  26 "    0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO C  27 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C  27 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  27 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  26 "   -0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO A  27 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  26 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B  27 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B  27 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  27 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1011 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 763
        2.76 -     3.29: 5555
        3.29 -     3.83: 9824
        3.83 -     4.36: 12312
        4.36 -     4.90: 20983
  Nonbonded interactions: 49437
  Sorted by model distance:
  nonbonded pdb=" N   GLY B 220 "
            pdb=" OE1 GLN B 234 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" N   GLY A 220 "
            pdb=" OE1 GLN A 234 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" N   GLY C 220 "
            pdb=" OE1 GLN C 234 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" O   ALA A 261 "
            pdb=" NZ  LYS B 272 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   LEU A 191 "
            pdb=" OG  SER A 195 "
     model   vdw
     2.278 3.040
  ... (remaining 49432 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.670
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6643
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      :  0.002   0.031   5538  Z= 0.128
  Angle     :  0.600  10.436   7467  Z= 0.331
  Chirality :  0.044   0.114    798
  Planarity :  0.003   0.038   1014
  Dihedral  : 16.589  89.148   1899
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 31.22 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.02 (0.29), residues: 744
  helix: -2.34 (0.48), residues: 84
  sheet:  0.11 (0.45), residues: 135
  loop : -1.67 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 269 
 HIS   0.002   0.001   HIS B  85 
 PHE   0.004   0.001   PHE A 138 
 TYR   0.013   0.002   TYR A 258 
 ARG   0.002   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28008 (  130)
  hydrogen bonds       : angle       9.17295 (  417)
  covalent geometry    : bond        0.00240 ( 5538)
  covalent geometry    : angle       0.60008 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.5726 (m-40) cc_final: 0.5411 (m-40)
REVERT: A   90 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6570 (mmtm)
REVERT: A  100 ASN cc_start: 0.6878 (m-40) cc_final: 0.6625 (m-40)
REVERT: A  130 VAL cc_start: 0.7695 (t) cc_final: 0.7221 (m)
REVERT: A  164 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7223 (mtmm)
REVERT: A  174 ILE cc_start: 0.8376 (mm) cc_final: 0.8072 (mm)
REVERT: A  194 ASN cc_start: 0.7790 (m-40) cc_final: 0.7579 (m-40)
REVERT: A  228 ASP cc_start: 0.7759 (m-30) cc_final: 0.7504 (m-30)
REVERT: B   70 THR cc_start: 0.8129 (m) cc_final: 0.7630 (p)
REVERT: B  100 ASN cc_start: 0.6736 (m-40) cc_final: 0.6511 (m-40)
REVERT: B  130 VAL cc_start: 0.7612 (t) cc_final: 0.7164 (m)
REVERT: B  150 LYS cc_start: 0.8102 (pttt) cc_final: 0.7145 (ptpp)
REVERT: B  171 ASP cc_start: 0.7386 (m-30) cc_final: 0.6720 (m-30)
REVERT: C  130 VAL cc_start: 0.7762 (t) cc_final: 0.7314 (m)
REVERT: C  150 LYS cc_start: 0.8130 (pttt) cc_final: 0.7235 (ptpp)
  outliers start: 6
  outliers final: 5
  residues processed: 145
  average time/residue: 0.1490
  time to fit residues: 29.3059
Evaluate side-chains
  109 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain C residue  128 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0030
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 129 GLN
A 133 ASN
A 154 ASN
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 HIS
B 133 ASN
B 172 ASN
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 216 ASN
C  44 ASN
C  85 HIS
C 161 ASN
C 216 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.120956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.108882 restraints weight = 8007.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.111494 restraints weight = 4551.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.113192 restraints weight = 2870.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5538  Z= 0.175
  Angle     :  0.593   7.197   7467  Z= 0.334
  Chirality :  0.050   0.149    798
  Planarity :  0.003   0.034   1014
  Dihedral  :  5.695  52.310    788
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 26.98 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.24 (0.27), residues: 744
  helix: -2.67 (0.38), residues: 90
  sheet:  0.17 (0.37), residues: 186
  loop : -2.06 (0.24), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 269 
 HIS   0.002   0.001   HIS A  85 
 PHE   0.011   0.001   PHE C 134 
 TYR   0.009   0.002   TYR C 157 
 ARG   0.003   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  130)
  hydrogen bonds       : angle       6.08869 (  417)
  covalent geometry    : bond        0.00371 ( 5538)
  covalent geometry    : angle       0.59276 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7705 (t) cc_final: 0.7462 (m)
REVERT: A  140 MET cc_start: 0.7279 (tmm) cc_final: 0.6414 (ttt)
REVERT: A  194 ASN cc_start: 0.7881 (m-40) cc_final: 0.7544 (m110)
REVERT: B   86 ASN cc_start: 0.7535 (m-40) cc_final: 0.7334 (m110)
REVERT: B   94 SER cc_start: 0.8150 (m) cc_final: 0.7501 (p)
REVERT: B  100 ASN cc_start: 0.7392 (m-40) cc_final: 0.6957 (m-40)
REVERT: B  120 ASN cc_start: 0.7449 (m-40) cc_final: 0.7199 (m-40)
REVERT: B  130 VAL cc_start: 0.7788 (t) cc_final: 0.7306 (m)
REVERT: B  149 TYR cc_start: 0.7532 (m-80) cc_final: 0.7178 (m-80)
REVERT: B  150 LYS cc_start: 0.8083 (pttt) cc_final: 0.7849 (ptpp)
REVERT: B  171 ASP cc_start: 0.7064 (m-30) cc_final: 0.6694 (m-30)
REVERT: B  193 ASN cc_start: 0.6872 (t0) cc_final: 0.6451 (t0)
REVERT: C   61 ILE cc_start: 0.5992 (mm) cc_final: 0.5771 (mm)
REVERT: C  120 ASN cc_start: 0.7813 (m-40) cc_final: 0.7454 (m-40)
  outliers start: 34
  outliers final: 18
  residues processed: 171
  average time/residue: 0.1445
  time to fit residues: 33.3409
Evaluate side-chains
  138 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  156 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 24 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   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  92 HIS
A 151 ASN
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 ASN
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 ASN
B 172 ASN
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 216 ASN
B 239 ASN
** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 154 ASN
C 180 HIS
C 194 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.118633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.106777 restraints weight = 8164.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.109239 restraints weight = 4804.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.111008 restraints weight = 3096.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5538  Z= 0.205
  Angle     :  0.597   6.619   7467  Z= 0.340
  Chirality :  0.051   0.158    798
  Planarity :  0.003   0.034   1014
  Dihedral  :  6.061  53.134    788
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 29.98 %
    Favored  : 65.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.43 (0.27), residues: 744
  helix: -2.63 (0.42), residues: 90
  sheet: -0.16 (0.37), residues: 183
  loop : -2.13 (0.24), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 246 
 HIS   0.019   0.003   HIS A  85 
 PHE   0.024   0.002   PHE C 134 
 TYR   0.014   0.002   TYR A 147 
 ARG   0.004   0.001   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  130)
  hydrogen bonds       : angle       5.97132 (  417)
  covalent geometry    : bond        0.00441 ( 5538)
  covalent geometry    : angle       0.59717 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.5640 (m-40) cc_final: 0.5396 (m-40)
REVERT: A   86 ASN cc_start: 0.7720 (m-40) cc_final: 0.7290 (m-40)
REVERT: A  130 VAL cc_start: 0.7722 (t) cc_final: 0.7404 (m)
REVERT: A  140 MET cc_start: 0.7194 (tmm) cc_final: 0.6767 (tmm)
REVERT: A  161 ASN cc_start: 0.6370 (t0) cc_final: 0.6150 (t0)
REVERT: A  164 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7739 (mtmm)
REVERT: B   94 SER cc_start: 0.8295 (m) cc_final: 0.7591 (p)
REVERT: B  130 VAL cc_start: 0.7732 (t) cc_final: 0.7223 (m)
REVERT: B  140 MET cc_start: 0.7090 (tmm) cc_final: 0.6356 (ttt)
REVERT: B  149 TYR cc_start: 0.7685 (m-80) cc_final: 0.7461 (m-80)
REVERT: B  150 LYS cc_start: 0.8299 (pttt) cc_final: 0.7863 (ptpp)
REVERT: B  171 ASP cc_start: 0.7049 (m-30) cc_final: 0.6654 (m-30)
REVERT: B  193 ASN cc_start: 0.6905 (t0) cc_final: 0.6612 (t0)
REVERT: B  194 ASN cc_start: 0.7651 (m-40) cc_final: 0.7451 (m-40)
REVERT: C   59 LYS cc_start: 0.6827 (mttm) cc_final: 0.6586 (mttm)
REVERT: C   86 ASN cc_start: 0.7754 (m-40) cc_final: 0.7462 (m110)
  outliers start: 24
  outliers final: 16
  residues processed: 151
  average time/residue: 0.1340
  time to fit residues: 27.8917
Evaluate side-chains
  138 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  150 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 72 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 ASN
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
C 194 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.108451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.097216 restraints weight = 8664.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.099537 restraints weight = 4801.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.101150 restraints weight = 2994.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5538  Z= 0.209
  Angle     :  0.576   6.322   7467  Z= 0.334
  Chirality :  0.050   0.149    798
  Planarity :  0.003   0.034   1014
  Dihedral  :  5.989  54.378    785
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 31.39 %
    Favored  : 64.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.70 (0.26), residues: 744
  helix: -2.66 (0.42), residues: 90
  sheet: -0.64 (0.41), residues: 147
  loop : -2.11 (0.23), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP C 246 
 HIS   0.007   0.002   HIS A  85 
 PHE   0.026   0.002   PHE A 134 
 TYR   0.014   0.003   TYR A  56 
 ARG   0.002   0.000   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03185 (  130)
  hydrogen bonds       : angle       5.94306 (  417)
  covalent geometry    : bond        0.00451 ( 5538)
  covalent geometry    : angle       0.57561 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.5858 (m-40) cc_final: 0.5585 (m-40)
REVERT: A   86 ASN cc_start: 0.7487 (m-40) cc_final: 0.7099 (m-40)
REVERT: A  128 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6863 (m-80)
REVERT: A  130 VAL cc_start: 0.7785 (t) cc_final: 0.7356 (m)
REVERT: A  150 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7935 (ptpt)
REVERT: A  164 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7718 (mtmm)
REVERT: B   45 VAL cc_start: 0.7099 (t) cc_final: 0.6826 (m)
REVERT: B   63 LYS cc_start: 0.7374 (ttpp) cc_final: 0.7135 (ttpp)
REVERT: B   90 LYS cc_start: 0.7612 (mttm) cc_final: 0.7269 (mttm)
REVERT: B   94 SER cc_start: 0.8264 (m) cc_final: 0.7572 (p)
REVERT: B  103 ASP cc_start: 0.7465 (m-30) cc_final: 0.6881 (m-30)
REVERT: B  117 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7596 (m)
REVERT: B  119 PHE cc_start: 0.8077 (t80) cc_final: 0.7793 (t80)
REVERT: B  128 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7217 (m-80)
REVERT: B  130 VAL cc_start: 0.7749 (t) cc_final: 0.7328 (m)
REVERT: B  140 MET cc_start: 0.7223 (tmm) cc_final: 0.5584 (ttt)
REVERT: B  149 TYR cc_start: 0.7717 (m-80) cc_final: 0.7476 (m-80)
REVERT: B  150 LYS cc_start: 0.8153 (pttt) cc_final: 0.7766 (ptpp)
REVERT: B  151 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7199 (m-40)
REVERT: B  171 ASP cc_start: 0.6942 (m-30) cc_final: 0.6715 (m-30)
REVERT: C   59 LYS cc_start: 0.6879 (mttm) cc_final: 0.6646 (mttm)
REVERT: C   86 ASN cc_start: 0.7810 (m-40) cc_final: 0.7362 (m110)
REVERT: C  120 ASN cc_start: 0.8000 (m-40) cc_final: 0.7703 (m-40)
  outliers start: 25
  outliers final: 15
  residues processed: 153
  average time/residue: 0.1528
  time to fit residues: 31.1488
Evaluate side-chains
  149 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  197 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 ASN
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 187 ASN
C 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.105222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.094364 restraints weight = 8770.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.096924 restraints weight = 4578.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.098613 restraints weight = 2696.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   5538  Z= 0.257
  Angle     :  0.605   6.540   7467  Z= 0.356
  Chirality :  0.052   0.151    798
  Planarity :  0.003   0.036   1014
  Dihedral  :  6.363  54.029    785
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 30.16 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.04 (0.25), residues: 744
  helix: -2.91 (0.40), residues: 93
  sheet: -1.02 (0.40), residues: 147
  loop : -2.29 (0.22), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 246 
 HIS   0.006   0.002   HIS B  92 
 PHE   0.025   0.003   PHE B 134 
 TYR   0.012   0.003   TYR A 147 
 ARG   0.002   0.000   ARG B 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  130)
  hydrogen bonds       : angle       5.96781 (  417)
  covalent geometry    : bond        0.00558 ( 5538)
  covalent geometry    : angle       0.60482 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.6270 (m-40) cc_final: 0.6067 (m-40)
REVERT: A  120 ASN cc_start: 0.7957 (m-40) cc_final: 0.7745 (m-40)
REVERT: A  128 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6810 (m-80)
REVERT: A  150 LYS cc_start: 0.8392 (ptpt) cc_final: 0.8110 (ptpt)
REVERT: A  159 ILE cc_start: 0.8128 (mt) cc_final: 0.7423 (tt)
REVERT: A  164 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7780 (mtmm)
REVERT: B   63 LYS cc_start: 0.7365 (ttpp) cc_final: 0.7088 (ttpp)
REVERT: B   90 LYS cc_start: 0.7597 (mttm) cc_final: 0.7089 (mttm)
REVERT: B  103 ASP cc_start: 0.7477 (m-30) cc_final: 0.6844 (m-30)
REVERT: B  117 SER cc_start: 0.7838 (m) cc_final: 0.7620 (m)
REVERT: B  128 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7265 (m-80)
REVERT: B  130 VAL cc_start: 0.7822 (t) cc_final: 0.7414 (m)
REVERT: B  150 LYS cc_start: 0.8241 (pttt) cc_final: 0.7699 (ptpp)
REVERT: B  171 ASP cc_start: 0.7186 (m-30) cc_final: 0.6951 (m-30)
REVERT: B  223 SER cc_start: 0.7819 (p) cc_final: 0.7331 (m)
REVERT: C   86 ASN cc_start: 0.7800 (m-40) cc_final: 0.7334 (m110)
REVERT: C  128 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6996 (m-80)
REVERT: C  151 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7512 (m-40)
REVERT: C  233 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7597 (ttp-170)
  outliers start: 30
  outliers final: 20
  residues processed: 172
  average time/residue: 0.1522
  time to fit residues: 34.7299
Evaluate side-chains
  155 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.107252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.096538 restraints weight = 8552.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.099117 restraints weight = 4463.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.100867 restraints weight = 2625.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   5538  Z= 0.286
  Angle     :  0.637   6.513   7467  Z= 0.373
  Chirality :  0.053   0.144    798
  Planarity :  0.003   0.037   1014
  Dihedral  :  6.494  53.067    785
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 31.57 %
    Favored  : 62.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.33 (0.25), residues: 744
  helix: -3.14 (0.39), residues: 93
  sheet: -1.29 (0.40), residues: 147
  loop : -2.46 (0.22), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 246 
 HIS   0.008   0.003   HIS C  92 
 PHE   0.029   0.003   PHE A 134 
 TYR   0.014   0.003   TYR A 128 
 ARG   0.003   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03654 (  130)
  hydrogen bonds       : angle       6.01873 (  417)
  covalent geometry    : bond        0.00623 ( 5538)
  covalent geometry    : angle       0.63703 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.6191 (m-40) cc_final: 0.5936 (m-40)
REVERT: A  100 ASN cc_start: 0.7485 (m-40) cc_final: 0.7143 (m-40)
REVERT: A  128 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6727 (m-80)
REVERT: A  130 VAL cc_start: 0.7971 (t) cc_final: 0.7629 (m)
REVERT: A  150 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8093 (ptpt)
REVERT: A  159 ILE cc_start: 0.8066 (mt) cc_final: 0.7535 (tt)
REVERT: B   63 LYS cc_start: 0.7357 (ttpp) cc_final: 0.7147 (ttpp)
REVERT: B   90 LYS cc_start: 0.7606 (mttm) cc_final: 0.7111 (mttm)
REVERT: B  117 SER cc_start: 0.7828 (m) cc_final: 0.7607 (m)
REVERT: B  128 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7453 (m-80)
REVERT: B  130 VAL cc_start: 0.7908 (t) cc_final: 0.7373 (m)
REVERT: B  148 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7554 (mm-40)
REVERT: B  150 LYS cc_start: 0.8241 (pttt) cc_final: 0.7809 (ptpp)
REVERT: B  158 MET cc_start: 0.6066 (mtm) cc_final: 0.5722 (mtm)
REVERT: B  159 ILE cc_start: 0.8181 (mp) cc_final: 0.7602 (tt)
REVERT: B  223 SER cc_start: 0.7976 (p) cc_final: 0.7474 (m)
REVERT: C   86 ASN cc_start: 0.7775 (m-40) cc_final: 0.7304 (m110)
REVERT: C  128 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7135 (m-80)
REVERT: C  233 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7601 (ttp-170)
  outliers start: 34
  outliers final: 26
  residues processed: 159
  average time/residue: 0.1619
  time to fit residues: 34.1024
Evaluate side-chains
  158 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0770
   chunk 45 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 73 optimal weight:    0.2980
   chunk 28 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 148 GLN
** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.109396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.098311 restraints weight = 8596.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.101033 restraints weight = 4439.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.102757 restraints weight = 2597.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.4907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5538  Z= 0.168
  Angle     :  0.571   7.001   7467  Z= 0.328
  Chirality :  0.050   0.148    798
  Planarity :  0.003   0.038   1014
  Dihedral  :  6.101  53.935    785
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 33.16 %
    Favored  : 61.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.30 (0.25), residues: 744
  helix: -3.07 (0.39), residues: 90
  sheet: -1.15 (0.40), residues: 147
  loop : -2.51 (0.21), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 269 
 HIS   0.005   0.002   HIS A 180 
 PHE   0.024   0.002   PHE C 134 
 TYR   0.014   0.002   TYR A 128 
 ARG   0.002   0.000   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02869 (  130)
  hydrogen bonds       : angle       5.81068 (  417)
  covalent geometry    : bond        0.00373 ( 5538)
  covalent geometry    : angle       0.57111 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.6085 (m-40) cc_final: 0.5845 (m-40)
REVERT: A  100 ASN cc_start: 0.7408 (m-40) cc_final: 0.7101 (m-40)
REVERT: A  128 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6770 (m-80)
REVERT: A  130 VAL cc_start: 0.7916 (t) cc_final: 0.7477 (m)
REVERT: A  134 PHE cc_start: 0.7269 (m-80) cc_final: 0.7045 (m-80)
REVERT: A  140 MET cc_start: 0.7176 (tmm) cc_final: 0.6321 (tmm)
REVERT: A  150 LYS cc_start: 0.8399 (ptpt) cc_final: 0.8126 (ptpt)
REVERT: A  159 ILE cc_start: 0.7962 (mt) cc_final: 0.7546 (tt)
REVERT: B   90 LYS cc_start: 0.7601 (mttm) cc_final: 0.7101 (mttm)
REVERT: B  117 SER cc_start: 0.7802 (m) cc_final: 0.7520 (m)
REVERT: B  128 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7407 (m-80)
REVERT: B  140 MET cc_start: 0.6996 (tmm) cc_final: 0.5755 (ttt)
REVERT: B  148 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7383 (mm-40)
REVERT: B  150 LYS cc_start: 0.8244 (pttt) cc_final: 0.7853 (ptpp)
REVERT: B  159 ILE cc_start: 0.8163 (mp) cc_final: 0.7621 (tt)
REVERT: B  223 SER cc_start: 0.7957 (p) cc_final: 0.7465 (m)
REVERT: C   86 ASN cc_start: 0.7764 (m-40) cc_final: 0.7271 (m110)
REVERT: C  233 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7661 (ttp-170)
  outliers start: 30
  outliers final: 21
  residues processed: 149
  average time/residue: 0.1553
  time to fit residues: 30.5548
Evaluate side-chains
  154 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 24 optimal weight:    0.2980
   chunk 66 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   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 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.109077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.097969 restraints weight = 8840.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.100933 restraints weight = 4391.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.102850 restraints weight = 2481.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5538  Z= 0.212
  Angle     :  0.594   6.361   7467  Z= 0.343
  Chirality :  0.051   0.154    798
  Planarity :  0.003   0.038   1014
  Dihedral  :  6.201  53.759    785
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 33.33 %
    Favored  : 61.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.38 (0.25), residues: 744
  helix: -3.12 (0.39), residues: 93
  sheet: -1.19 (0.40), residues: 147
  loop : -2.57 (0.21), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP C 246 
 HIS   0.006   0.002   HIS C  92 
 PHE   0.028   0.002   PHE B 134 
 TYR   0.013   0.002   TYR B  56 
 ARG   0.002   0.000   ARG B 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03057 (  130)
  hydrogen bonds       : angle       5.84314 (  417)
  covalent geometry    : bond        0.00468 ( 5538)
  covalent geometry    : angle       0.59408 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.6117 (m-40) cc_final: 0.5894 (m-40)
REVERT: A   90 LYS cc_start: 0.6723 (mmtm) cc_final: 0.6510 (mmtm)
REVERT: A  100 ASN cc_start: 0.7372 (m-40) cc_final: 0.7084 (m-40)
REVERT: A  128 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6790 (m-80)
REVERT: A  130 VAL cc_start: 0.7939 (t) cc_final: 0.7476 (m)
REVERT: A  150 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8139 (ptpt)
REVERT: A  159 ILE cc_start: 0.7953 (mt) cc_final: 0.7561 (tt)
REVERT: B   90 LYS cc_start: 0.7600 (mttm) cc_final: 0.7064 (mttm)
REVERT: B  117 SER cc_start: 0.7789 (m) cc_final: 0.7565 (m)
REVERT: B  128 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7442 (m-80)
REVERT: B  148 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7456 (mm-40)
REVERT: B  150 LYS cc_start: 0.8288 (pttt) cc_final: 0.7804 (ptpp)
REVERT: B  158 MET cc_start: 0.6216 (mtm) cc_final: 0.5937 (mtm)
REVERT: B  159 ILE cc_start: 0.8183 (mp) cc_final: 0.7617 (tt)
REVERT: B  223 SER cc_start: 0.8002 (p) cc_final: 0.7491 (m)
REVERT: C   86 ASN cc_start: 0.7747 (m-40) cc_final: 0.7304 (m110)
REVERT: C  115 THR cc_start: 0.8406 (m) cc_final: 0.8021 (t)
REVERT: C  128 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6759 (m-80)
REVERT: C  233 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7625 (ttp-170)
  outliers start: 28
  outliers final: 21
  residues processed: 157
  average time/residue: 0.1490
  time to fit residues: 31.0685
Evaluate side-chains
  155 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0030
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
** B  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 HIS
** B  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 HIS
** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.108426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.097471 restraints weight = 8922.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.100412 restraints weight = 4416.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.102261 restraints weight = 2488.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.5209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5538  Z= 0.207
  Angle     :  0.589   6.395   7467  Z= 0.341
  Chirality :  0.050   0.152    798
  Planarity :  0.003   0.038   1014
  Dihedral  :  6.220  53.943    785
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 33.16 %
    Favored  : 61.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.24), residues: 744
  helix: -3.10 (0.39), residues: 93
  sheet: -1.24 (0.40), residues: 147
  loop : -2.61 (0.21), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP C 246 
 HIS   0.007   0.002   HIS C  92 
 PHE   0.029   0.003   PHE B 134 
 TYR   0.014   0.002   TYR B  56 
 ARG   0.001   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03112 (  130)
  hydrogen bonds       : angle       5.87963 (  417)
  covalent geometry    : bond        0.00456 ( 5538)
  covalent geometry    : angle       0.58900 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.6077 (m-40) cc_final: 0.5861 (m-40)
REVERT: A   90 LYS cc_start: 0.6870 (mmtm) cc_final: 0.6439 (mmtm)
REVERT: A  100 ASN cc_start: 0.7396 (m-40) cc_final: 0.7040 (m-40)
REVERT: A  114 ASN cc_start: 0.7771 (m-40) cc_final: 0.7410 (m-40)
REVERT: A  128 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6693 (m-80)
REVERT: A  130 VAL cc_start: 0.7944 (t) cc_final: 0.7496 (m)
REVERT: A  150 LYS cc_start: 0.8401 (ptpt) cc_final: 0.8128 (ptpt)
REVERT: A  159 ILE cc_start: 0.7915 (mt) cc_final: 0.7543 (tt)
REVERT: B   59 LYS cc_start: 0.7580 (mmtp) cc_final: 0.7228 (mmtp)
REVERT: B   90 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7006 (mttm)
REVERT: B  117 SER cc_start: 0.7794 (m) cc_final: 0.7576 (m)
REVERT: B  128 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7490 (m-80)
REVERT: B  130 VAL cc_start: 0.7879 (t) cc_final: 0.7344 (m)
REVERT: B  140 MET cc_start: 0.6989 (tmm) cc_final: 0.5813 (ttt)
REVERT: B  148 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7403 (mm-40)
REVERT: B  150 LYS cc_start: 0.8285 (pttt) cc_final: 0.7807 (ptpp)
REVERT: B  158 MET cc_start: 0.6131 (mtm) cc_final: 0.5863 (mtm)
REVERT: B  159 ILE cc_start: 0.8166 (mp) cc_final: 0.7645 (tt)
REVERT: B  223 SER cc_start: 0.8003 (p) cc_final: 0.7484 (m)
REVERT: C   59 LYS cc_start: 0.7175 (mttm) cc_final: 0.6952 (mttp)
REVERT: C  233 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7636 (ttp-170)
  outliers start: 33
  outliers final: 27
  residues processed: 156
  average time/residue: 0.1514
  time to fit residues: 31.5921
Evaluate side-chains
  157 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
** B  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 HIS
** C 177 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 = 0.3561 r_free = 0.3561 target = 0.105854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.095770 restraints weight = 8982.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.098408 restraints weight = 4543.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.100131 restraints weight = 2606.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.5357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   5538  Z= 0.271
  Angle     :  0.627   6.455   7467  Z= 0.365
  Chirality :  0.052   0.166    798
  Planarity :  0.003   0.037   1014
  Dihedral  :  6.404  53.567    785
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 34.04 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.55 (0.24), residues: 744
  helix: -3.12 (0.39), residues: 93
  sheet: -1.36 (0.40), residues: 147
  loop : -2.70 (0.21), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 246 
 HIS   0.015   0.004   HIS B  85 
 PHE   0.028   0.003   PHE B  84 
 TYR   0.016   0.003   TYR C 258 
 ARG   0.002   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03476 (  130)
  hydrogen bonds       : angle       5.96093 (  417)
  covalent geometry    : bond        0.00599 ( 5538)
  covalent geometry    : angle       0.62715 ( 7467)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.6128 (m-40) cc_final: 0.5903 (m-40)
REVERT: A   90 LYS cc_start: 0.6996 (mmtm) cc_final: 0.6669 (mmtm)
REVERT: A  100 ASN cc_start: 0.7355 (m-40) cc_final: 0.6949 (m-40)
REVERT: A  128 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6740 (m-80)
REVERT: A  130 VAL cc_start: 0.7969 (t) cc_final: 0.7609 (m)
REVERT: A  150 LYS cc_start: 0.8374 (ptpt) cc_final: 0.8115 (ptpt)
REVERT: A  159 ILE cc_start: 0.7941 (mt) cc_final: 0.7592 (tt)
REVERT: B   59 LYS cc_start: 0.7582 (mmtp) cc_final: 0.7249 (mmtp)
REVERT: B   90 LYS cc_start: 0.7654 (mmtm) cc_final: 0.7094 (mttm)
REVERT: B  117 SER cc_start: 0.7803 (m) cc_final: 0.7576 (m)
REVERT: B  128 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7554 (m-80)
REVERT: B  130 VAL cc_start: 0.7898 (t) cc_final: 0.7365 (m)
REVERT: B  140 MET cc_start: 0.7114 (tmm) cc_final: 0.5938 (ttt)
REVERT: B  148 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7433 (mm-40)
REVERT: B  150 LYS cc_start: 0.8255 (pttt) cc_final: 0.7849 (ptpp)
REVERT: B  158 MET cc_start: 0.6141 (mtm) cc_final: 0.5885 (mtm)
REVERT: B  159 ILE cc_start: 0.8184 (mp) cc_final: 0.7677 (tt)
REVERT: B  223 SER cc_start: 0.8004 (p) cc_final: 0.7508 (m)
REVERT: C   59 LYS cc_start: 0.7181 (mttm) cc_final: 0.6852 (mttm)
REVERT: C  128 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.6896 (m-80)
REVERT: C  140 MET cc_start: 0.6956 (tmm) cc_final: 0.5787 (tmm)
REVERT: C  233 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7652 (ttp-170)
  outliers start: 29
  outliers final: 25
  residues processed: 146
  average time/residue: 0.1772
  time to fit residues: 33.7534
Evaluate side-chains
  156 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0770
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
** B  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 HIS
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 HIS
** C 177 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 = 0.3561 r_free = 0.3561 target = 0.105371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.094328 restraints weight = 8961.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.097280 restraints weight = 4385.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.099213 restraints weight = 2468.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5538  Z= 0.228
  Angle     :  0.610   6.223   7467  Z= 0.353
  Chirality :  0.051   0.153    798
  Planarity :  0.003   0.037   1014
  Dihedral  :  6.333  53.622    785
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 34.04 %
    Favored  : 60.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.55 (0.24), residues: 744
  helix: -2.92 (0.43), residues: 84
  sheet: -1.39 (0.39), residues: 147
  loop : -2.74 (0.20), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 246 
 HIS   0.010   0.003   HIS C  85 
 PHE   0.028   0.003   PHE B  84 
 TYR   0.014   0.002   TYR B  56 
 ARG   0.009   0.001   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03238 (  130)
  hydrogen bonds       : angle       5.92431 (  417)
  covalent geometry    : bond        0.00504 ( 5538)
  covalent geometry    : angle       0.61026 ( 7467)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2227.75 seconds
wall clock time: 39 minutes 28.34 seconds (2368.34 seconds total)