Starting phenix.real_space_refine
on Wed Sep 17 06:31:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mrr_48562/09_2025/9mrr_48562_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mrr_48562/09_2025/9mrr_48562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mrr_48562/09_2025/9mrr_48562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mrr_48562/09_2025/9mrr_48562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mrr_48562/09_2025/9mrr_48562_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mrr_48562/09_2025/9mrr_48562_neut.cif"
  }
  resolution = 4.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.025
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      25      5.16       5
     C    4067      2.51       5
     N     920      2.21       5
     O    1036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6048
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1504
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 4, 'TRANS': 179}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1528
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 5, 'TRANS': 181}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1504
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 4, 'TRANS': 179}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1512
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 4, 'TRANS': 180}
          Chain breaks: 1
  Time building chain proxies: 1.55, per 1000 atoms: 0.26
  Number of scatterers: 6048
  At special positions: 0
  Unit cell: (81.928, 84.056, 82.992, 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      25     16.00
     O    1036      8.00
     N     920      7.00
     C    4067      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 174.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1416

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      54.1% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 28
      removed outlier: 4.325A  pdb=" N   LEU A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TYR A  12 " --> pdb=" O   LYS A   8 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   MET A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   LEU A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ILE A  25 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 50
    Processing helix  chain 'A' and resid 50 through 76
      removed outlier: 3.883A  pdb=" N   ILE A  54 " --> pdb=" O   ASN A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 108
      removed outlier: 4.267A  pdb=" N   VAL A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      Proline residue:  A 104  - end of helix
    Processing helix  chain 'A' and resid 112 through 133
      removed outlier: 3.759A  pdb=" N   ALA A 118 " --> pdb=" O   GLN A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.614A  pdb=" N   PHE A 145 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 16
    Processing helix  chain 'B' and resid 16 through 28
    Processing helix  chain 'B' and resid 43 through 49
    Processing helix  chain 'B' and resid 50 through 76
    Processing helix  chain 'B' and resid 95 through 102
    Processing helix  chain 'B' and resid 112 through 132
    Processing helix  chain 'B' and resid 142 through 146
    Processing helix  chain 'C' and resid 2 through 16
      removed outlier: 3.874A  pdb=" N   TYR C   6 " --> pdb=" O   GLN C   2 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASN C   7 " --> pdb=" O   ARG C   3 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY C  10 " --> pdb=" O   TYR C   6 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU C  11 " --> pdb=" O   ASN C   7 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   TYR C  12 " --> pdb=" O   LYS C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 27
      removed outlier: 3.542A  pdb=" N   PHE C  20 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL C  21 " --> pdb=" O   ALA C  17 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE C  22 " --> pdb=" O   MET C  18 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE C  24 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ILE C  25 " --> pdb=" O   VAL C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 50
      removed outlier: 3.615A  pdb=" N   VAL C  47 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN C  50 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 75
      removed outlier: 3.647A  pdb=" N   ILE C  54 " --> pdb=" O   ASN C  50 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   CYS C  56 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   VAL C  58 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE C  59 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 108
    Processing helix  chain 'C' and resid 112 through 133
      removed outlier: 3.608A  pdb=" N   ASN C 116 " --> pdb=" O   ASP C 112 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE C 129 " --> pdb=" O   VAL C 125 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS C 132 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 144
      removed outlier: 3.521A  pdb=" N   ALA C 143 " --> pdb=" O   ASN C 139 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 7
      removed outlier: 4.293A  pdb=" N   ASN D   7 " --> pdb=" O   ARG D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 16
      removed outlier: 4.209A  pdb=" N   LEU D  11 " --> pdb=" O   ASN D   7 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   TYR D  12 " --> pdb=" O   LYS D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 27
      removed outlier: 3.706A  pdb=" N   VAL D  21 " --> pdb=" O   ALA D  17 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   PHE D  22 " --> pdb=" O   MET D  18 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ILE D  23 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE D  24 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE D  25 " --> pdb=" O   VAL D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 50
    Processing helix  chain 'D' and resid 50 through 74
      removed outlier: 4.166A  pdb=" N   ILE D  54 " --> pdb=" O   ASN D  50 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL D  55 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   VAL D  58 " --> pdb=" O   ILE D  54 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   PHE D  59 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE D  60 " --> pdb=" O   CYS D  56 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   THR D  74 " --> pdb=" O   LEU D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 96
      No H-bonds generated for 'chain 'D' and resid 94 through 96'
    Processing helix  chain 'D' and resid 97 through 102
      removed outlier: 3.723A  pdb=" N   ILE D 102 " --> pdb=" O   LEU D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 133
      removed outlier: 3.904A  pdb=" N   ALA D 118 " --> pdb=" O   GLN D 114 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL D 124 " --> pdb=" O   LEU D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 139
      removed outlier: 3.859A  pdb=" N   ASN D 139 " --> pdb=" O   TYR D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 146
    Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 152
      removed outlier: 3.557A  pdb=" N   SER A 169 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   PHE A 189 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 156
    Processing sheet with id=AA3, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.650A  pdb=" N   SER B 169 " --> pdb=" O   LYS B 148 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TYR B 150 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ILE B 166 " --> pdb=" O   PHE B 189 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ALA B 191 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ILE B 168 " --> pdb=" O   ALA B 191 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 148 through 152
      removed outlier: 3.726A  pdb=" N   SER C 169 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE C 166 " --> pdb=" O   PHE C 189 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   ALA C 191 " --> pdb=" O   ILE C 166 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ILE C 168 " --> pdb=" O   ALA C 191 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 148 through 152
    Processing sheet with id=AA6, first strand: chain 'D' and resid 181 through 183

    263 hydrogen bonds defined for protein.
    747 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: 0.62

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1705
        1.34 -     1.46: 1444
        1.46 -     1.58: 2996
        1.58 -     1.70: 0
        1.70 -     1.82: 41
  Bond restraints: 6186
  Sorted by residual:
  bond pdb=" C   VAL D 103 "
       pdb=" N   PRO D 104 "
    ideal  model  delta    sigma   weight residual
    1.337  1.374 -0.038 1.11e-02 8.12e+03 1.17e+01
  bond pdb=" C   VAL A  52 "
       pdb=" N   PRO A  53 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.033 1.36e-02 5.41e+03 5.72e+00
  bond pdb=" C   VAL C 103 "
       pdb=" N   PRO C 104 "
    ideal  model  delta    sigma   weight residual
    1.337  1.361 -0.024 1.11e-02 8.12e+03 4.82e+00
  bond pdb=" CA  ASN B 164 "
       pdb=" CB  ASN B 164 "
    ideal  model  delta    sigma   weight residual
    1.527  1.562 -0.035 1.70e-02 3.46e+03 4.16e+00
  bond pdb=" CB  ASN B 164 "
       pdb=" CG  ASN B 164 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.42e+00
  ... (remaining 6181 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 7834
        2.16 -     4.33: 402
        4.33 -     6.49: 88
        6.49 -     8.66: 27
        8.66 -    10.82: 12
  Bond angle restraints: 8363
  Sorted by residual:
  angle pdb=" C   ILE A 102 "
        pdb=" N   VAL A 103 "
        pdb=" CA  VAL A 103 "
      ideal   model   delta    sigma   weight residual
     120.24  125.75   -5.51 6.30e-01 2.52e+00 7.66e+01
  angle pdb=" C   VAL B 175 "
        pdb=" N   ASP B 176 "
        pdb=" CA  ASP B 176 "
      ideal   model   delta    sigma   weight residual
     121.54  132.13  -10.59 1.91e+00 2.74e-01 3.08e+01
  angle pdb=" C   VAL B  82 "
        pdb=" N   LYS B  83 "
        pdb=" CA  LYS B  83 "
      ideal   model   delta    sigma   weight residual
     121.54  130.89   -9.35 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   LYS A 163 "
        pdb=" N   ASN A 164 "
        pdb=" CA  ASN A 164 "
      ideal   model   delta    sigma   weight residual
     121.54  130.27   -8.73 1.91e+00 2.74e-01 2.09e+01
  angle pdb=" CG1 VAL A  82 "
        pdb=" CB  VAL A  82 "
        pdb=" CG2 VAL A  82 "
      ideal   model   delta    sigma   weight residual
     110.80  100.77   10.03 2.20e+00 2.07e-01 2.08e+01
  ... (remaining 8358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.09: 3141
       14.09 -    28.17: 375
       28.17 -    42.26: 97
       42.26 -    56.35: 18
       56.35 -    70.43: 1
  Dihedral angle restraints: 3632
    sinusoidal: 1432
      harmonic: 2200
  Sorted by residual:
  dihedral pdb=" CA  PHE C 183 "
           pdb=" C   PHE C 183 "
           pdb=" N   PHE C 184 "
           pdb=" CA  PHE C 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.63   28.37     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" CA  SER D  81 "
           pdb=" C   SER D  81 "
           pdb=" N   VAL D  82 "
           pdb=" CA  VAL D  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.11  -25.89     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  LYS C 148 "
           pdb=" C   LYS C 148 "
           pdb=" N   LEU C 149 "
           pdb=" CA  LEU C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.29  -23.71     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 3629 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 725
       0.064 -    0.128: 188
       0.128 -    0.192: 50
       0.192 -    0.256: 12
       0.256 -    0.320: 6
  Chirality restraints: 981
  Sorted by residual:
  chirality pdb=" CB  ILE A 168 "
            pdb=" CA  ILE A 168 "
            pdb=" CG1 ILE A 168 "
            pdb=" CG2 ILE A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  ASN B 164 "
            pdb=" N   ASN B 164 "
            pdb=" C   ASN B 164 "
            pdb=" CB  ASN B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.34e+00
  chirality pdb=" CB  VAL A  52 "
            pdb=" CA  VAL A  52 "
            pdb=" CG1 VAL A  52 "
            pdb=" CG2 VAL A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.24e+00
  ... (remaining 978 not shown)

  Planarity restraints: 1006
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  22 "    0.018 2.00e-02 2.50e+03   2.53e-02 1.12e+01
        pdb=" CG  PHE A  22 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  22 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  22 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  22 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  22 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  22 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 119 "   -0.013 2.00e-02 2.50e+03   2.33e-02 1.08e+01
        pdb=" CG  TYR A 119 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 119 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 119 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 119 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 119 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 119 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 119 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 106 "    0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   MET B 106 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   MET B 106 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLY B 107 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1003 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1858
        2.82 -     3.34: 5995
        3.34 -     3.86: 9971
        3.86 -     4.38: 11517
        4.38 -     4.90: 18433
  Nonbonded interactions: 47774
  Sorted by model distance:
  nonbonded pdb=" O   PHE B  60 "
            pdb=" OG  SER B  63 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER D 169 "
            pdb=" OD1 ASP D 171 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OG  SER B  15 "
            pdb=" OD1 ASN B 139 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   PHE C  60 "
            pdb=" OG  SER C  63 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER D 109 "
            pdb=" OG  SER D 109 "
     model   vdw
     2.330 3.040
  ... (remaining 47769 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 1 through 30 or resid 42 through 195))
  selection = chain 'C'
  selection = (chain 'D' and (resid 1 through 30 or resid 42 through 195))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.500
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
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      :  0.006   0.080   6186  Z= 0.266
  Angle     :  1.207  10.822   8363  Z= 0.651
  Chirality :  0.068   0.320    981
  Planarity :  0.008   0.081   1006
  Dihedral  : 13.135  70.433   2216
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.81 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.63 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.14 (0.24), residues: 724
  helix: -2.30 (0.21), residues: 357
  sheet: -2.16 (0.70), residues: 54
  loop : -3.35 (0.26), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 192 
 TYR   0.052   0.003   TYR A 119 
 PHE   0.056   0.004   PHE A  22 
 HIS   0.002   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 6186)
  covalent geometry    : angle       1.20685 ( 8363)
  hydrogen bonds       : bond        0.22050 (  263)
  hydrogen bonds       : angle       8.28080 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 264
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.9718 (mt) cc_final: 0.9439 (mt)
REVERT: A   20 PHE cc_start: 0.9437 (m-80) cc_final: 0.9171 (m-10)
REVERT: A   62 PHE cc_start: 0.8991 (m-10) cc_final: 0.8700 (m-10)
REVERT: A  119 TYR cc_start: 0.7890 (m-80) cc_final: 0.7679 (m-80)
REVERT: A  120 LEU cc_start: 0.9381 (mm) cc_final: 0.8977 (tt)
REVERT: A  136 TYR cc_start: 0.8206 (p90) cc_final: 0.7885 (p90)
REVERT: A  139 ASN cc_start: 0.8249 (t0) cc_final: 0.7781 (t0)
REVERT: A  141 THR cc_start: 0.9190 (m) cc_final: 0.8840 (m)
REVERT: B   77 ASN cc_start: 0.8508 (t0) cc_final: 0.8275 (m-40)
REVERT: B  181 TYR cc_start: 0.8664 (p90) cc_final: 0.8002 (p90)
REVERT: C    6 TYR cc_start: 0.7150 (m-10) cc_final: 0.6764 (m-80)
REVERT: C  134 ASP cc_start: 0.9228 (t70) cc_final: 0.8797 (t0)
REVERT: C  148 LYS cc_start: 0.8331 (pptt) cc_final: 0.8031 (pptt)
REVERT: C  173 LEU cc_start: 0.8144 (mm) cc_final: 0.7137 (tp)
REVERT: D   73 ILE cc_start: 0.9157 (mm) cc_final: 0.8685 (mm)
REVERT: D  113 MET cc_start: 0.7182 (pmm) cc_final: 0.6971 (pmm)
REVERT: D  119 TYR cc_start: 0.7693 (m-80) cc_final: 0.7123 (m-80)
REVERT: D  121 LEU cc_start: 0.9476 (tp) cc_final: 0.9035 (tp)
REVERT: D  153 ASN cc_start: 0.9044 (p0) cc_final: 0.8633 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 266
  average time/residue: 0.0463
  time to fit residues: 18.1919
Evaluate side-chains
  214 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
B 116 ASN
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 116 ASN
** C 164 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 = 0.3908 r_free = 0.3908 target = 0.119763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.095843 restraints weight = 17214.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.099254 restraints weight = 11017.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.101697 restraints weight = 7934.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.103506 restraints weight = 6203.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.104704 restraints weight = 5128.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6186  Z= 0.133
  Angle     :  0.678   7.325   8363  Z= 0.364
  Chirality :  0.044   0.159    981
  Planarity :  0.005   0.049   1006
  Dihedral  :  5.803  27.526    800
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  5.03 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (0.28), residues: 724
  helix: -1.00 (0.25), residues: 357
  sheet: -2.00 (0.67), residues: 66
  loop : -3.15 (0.29), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 192 
 TYR   0.026   0.002   TYR C 119 
 PHE   0.042   0.002   PHE A  97 
 HIS   0.001   0.000   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6186)
  covalent geometry    : angle       0.67761 ( 8363)
  hydrogen bonds       : bond        0.04440 (  263)
  hydrogen bonds       : angle       5.72019 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 264
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8851 (tpt) cc_final: 0.8275 (ptt)
REVERT: A   20 PHE cc_start: 0.9429 (m-80) cc_final: 0.9033 (m-80)
REVERT: A   22 PHE cc_start: 0.9042 (m-80) cc_final: 0.8840 (m-80)
REVERT: A   62 PHE cc_start: 0.8958 (m-10) cc_final: 0.8668 (m-10)
REVERT: A  139 ASN cc_start: 0.8063 (t160) cc_final: 0.7610 (t0)
REVERT: A  141 THR cc_start: 0.9282 (m) cc_final: 0.8468 (m)
REVERT: B    1 MET cc_start: 0.4985 (tmm) cc_final: 0.4699 (tmm)
REVERT: B   77 ASN cc_start: 0.8363 (t0) cc_final: 0.8060 (m-40)
REVERT: B  181 TYR cc_start: 0.8637 (p90) cc_final: 0.8182 (p90)
REVERT: C    6 TYR cc_start: 0.7018 (m-10) cc_final: 0.6714 (m-80)
REVERT: C   65 TYR cc_start: 0.8696 (t80) cc_final: 0.8446 (t80)
REVERT: C  112 ASP cc_start: 0.8524 (t70) cc_final: 0.7780 (t70)
REVERT: C  113 MET cc_start: 0.8046 (ptp) cc_final: 0.7397 (pmm)
REVERT: C  134 ASP cc_start: 0.9132 (t70) cc_final: 0.8707 (t0)
REVERT: C  173 LEU cc_start: 0.8010 (mm) cc_final: 0.7193 (tp)
REVERT: C  177 ASP cc_start: 0.8507 (p0) cc_final: 0.7675 (p0)
REVERT: C  179 VAL cc_start: 0.7583 (m) cc_final: 0.7205 (m)
REVERT: D   73 ILE cc_start: 0.9037 (mm) cc_final: 0.8646 (mm)
REVERT: D  113 MET cc_start: 0.7750 (pmm) cc_final: 0.7517 (pmm)
REVERT: D  114 GLN cc_start: 0.9316 (tt0) cc_final: 0.9074 (tt0)
REVERT: D  119 TYR cc_start: 0.7367 (m-80) cc_final: 0.6803 (m-80)
REVERT: D  147 PHE cc_start: 0.8632 (m-10) cc_final: 0.8420 (m-10)
REVERT: D  153 ASN cc_start: 0.9070 (p0) cc_final: 0.8500 (p0)
  outliers start: 4
  outliers final: 0
  residues processed: 264
  average time/residue: 0.0481
  time to fit residues: 19.0094
Evaluate side-chains
  212 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0970
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
B 116 ASN
C  50 ASN
D 116 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.120507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.096340 restraints weight = 17152.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.099725 restraints weight = 11095.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.102225 restraints weight = 8107.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.103949 restraints weight = 6392.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.105308 restraints weight = 5341.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6186  Z= 0.121
  Angle     :  0.642   7.221   8363  Z= 0.345
  Chirality :  0.044   0.167    981
  Planarity :  0.004   0.046   1006
  Dihedral  :  5.471  28.217    800
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  4.29 %
    Favored  : 95.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.56 (0.29), residues: 724
  helix: -0.54 (0.26), residues: 363
  sheet: -2.15 (0.65), residues: 72
  loop : -3.10 (0.29), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 192 
 TYR   0.022   0.001   TYR C 119 
 PHE   0.041   0.002   PHE A  97 
 HIS   0.001   0.000   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6186)
  covalent geometry    : angle       0.64217 ( 8363)
  hydrogen bonds       : bond        0.03930 (  263)
  hydrogen bonds       : angle       5.33258 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 268
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.9665 (mt) cc_final: 0.9187 (mt)
REVERT: A   18 MET cc_start: 0.8947 (tpt) cc_final: 0.8258 (tpt)
REVERT: A   20 PHE cc_start: 0.9431 (m-80) cc_final: 0.9078 (m-80)
REVERT: A   22 PHE cc_start: 0.9099 (m-80) cc_final: 0.8558 (m-80)
REVERT: A   62 PHE cc_start: 0.8939 (m-10) cc_final: 0.8674 (m-10)
REVERT: A  139 ASN cc_start: 0.8226 (t160) cc_final: 0.7930 (t160)
REVERT: B    1 MET cc_start: 0.5062 (tmm) cc_final: 0.4778 (tmm)
REVERT: B   50 ASN cc_start: 0.9519 (t0) cc_final: 0.9314 (t0)
REVERT: B   98 LEU cc_start: 0.9008 (tt) cc_final: 0.8808 (tp)
REVERT: B  128 ILE cc_start: 0.9285 (tt) cc_final: 0.8980 (tp)
REVERT: B  181 TYR cc_start: 0.8704 (p90) cc_final: 0.8271 (p90)
REVERT: C    6 TYR cc_start: 0.7051 (m-10) cc_final: 0.6756 (m-80)
REVERT: C   18 MET cc_start: 0.8782 (ppp) cc_final: 0.7518 (ppp)
REVERT: C   65 TYR cc_start: 0.8624 (t80) cc_final: 0.8329 (t80)
REVERT: C  112 ASP cc_start: 0.8367 (t70) cc_final: 0.7722 (t70)
REVERT: C  113 MET cc_start: 0.8263 (ptp) cc_final: 0.7576 (pmm)
REVERT: C  134 ASP cc_start: 0.9178 (t70) cc_final: 0.8719 (t0)
REVERT: C  155 LEU cc_start: 0.9193 (tp) cc_final: 0.8987 (tp)
REVERT: C  171 ASP cc_start: 0.8839 (p0) cc_final: 0.8611 (p0)
REVERT: C  173 LEU cc_start: 0.7956 (mm) cc_final: 0.7234 (tp)
REVERT: C  177 ASP cc_start: 0.8483 (p0) cc_final: 0.7671 (p0)
REVERT: C  179 VAL cc_start: 0.7341 (m) cc_final: 0.6975 (m)
REVERT: D   72 ASN cc_start: 0.9294 (m-40) cc_final: 0.8925 (m-40)
REVERT: D   73 ILE cc_start: 0.9020 (mm) cc_final: 0.8690 (mm)
REVERT: D  113 MET cc_start: 0.7765 (pmm) cc_final: 0.7498 (pmm)
REVERT: D  114 GLN cc_start: 0.9295 (tt0) cc_final: 0.9036 (tt0)
REVERT: D  119 TYR cc_start: 0.7148 (m-80) cc_final: 0.6747 (m-80)
REVERT: D  136 TYR cc_start: 0.8266 (p90) cc_final: 0.8061 (p90)
REVERT: D  142 LEU cc_start: 0.9237 (mt) cc_final: 0.8637 (mt)
REVERT: D  145 PHE cc_start: 0.8932 (m-10) cc_final: 0.8582 (m-10)
REVERT: D  147 PHE cc_start: 0.8178 (m-10) cc_final: 0.7136 (m-80)
REVERT: D  153 ASN cc_start: 0.9070 (p0) cc_final: 0.8422 (p0)
  outliers start: 4
  outliers final: 0
  residues processed: 269
  average time/residue: 0.0533
  time to fit residues: 20.6726
Evaluate side-chains
  220 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 21 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
B 116 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.120142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.096320 restraints weight = 17773.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.099667 restraints weight = 11483.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.102087 restraints weight = 8390.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.103779 restraints weight = 6632.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.104895 restraints weight = 5576.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6186  Z= 0.134
  Angle     :  0.651   7.332   8363  Z= 0.349
  Chirality :  0.044   0.154    981
  Planarity :  0.004   0.042   1006
  Dihedral  :  5.336  27.836    800
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.29 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.29), residues: 724
  helix: -0.32 (0.26), residues: 363
  sheet: -2.13 (0.62), residues: 77
  loop : -3.07 (0.30), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 192 
 TYR   0.024   0.002   TYR A 119 
 PHE   0.042   0.002   PHE A  97 
 HIS   0.001   0.000   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6186)
  covalent geometry    : angle       0.65145 ( 8363)
  hydrogen bonds       : bond        0.03750 (  263)
  hydrogen bonds       : angle       5.31209 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 272
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8840 (tpt) cc_final: 0.8167 (tpt)
REVERT: A   20 PHE cc_start: 0.9451 (m-80) cc_final: 0.9188 (m-80)
REVERT: A   22 PHE cc_start: 0.9167 (m-80) cc_final: 0.8616 (m-80)
REVERT: A   62 PHE cc_start: 0.8975 (m-10) cc_final: 0.8699 (m-10)
REVERT: B    1 MET cc_start: 0.5087 (tmm) cc_final: 0.4765 (tmm)
REVERT: B   50 ASN cc_start: 0.9513 (t0) cc_final: 0.9296 (t0)
REVERT: B  128 ILE cc_start: 0.9318 (tt) cc_final: 0.9016 (tp)
REVERT: B  161 GLU cc_start: 0.7937 (tp30) cc_final: 0.7308 (tp30)
REVERT: C    6 TYR cc_start: 0.7056 (m-10) cc_final: 0.6746 (m-80)
REVERT: C   18 MET cc_start: 0.8690 (ppp) cc_final: 0.8195 (ppp)
REVERT: C   65 TYR cc_start: 0.8627 (t80) cc_final: 0.8366 (t80)
REVERT: C  112 ASP cc_start: 0.8350 (t70) cc_final: 0.7828 (t70)
REVERT: C  113 MET cc_start: 0.8258 (ptp) cc_final: 0.7662 (pmm)
REVERT: C  134 ASP cc_start: 0.9198 (t70) cc_final: 0.8624 (t0)
REVERT: C  155 LEU cc_start: 0.9140 (tp) cc_final: 0.8910 (tp)
REVERT: C  171 ASP cc_start: 0.8964 (p0) cc_final: 0.8703 (p0)
REVERT: C  173 LEU cc_start: 0.8135 (mm) cc_final: 0.7455 (tp)
REVERT: C  177 ASP cc_start: 0.8515 (p0) cc_final: 0.7730 (p0)
REVERT: C  179 VAL cc_start: 0.7610 (m) cc_final: 0.7174 (m)
REVERT: D   72 ASN cc_start: 0.9301 (m-40) cc_final: 0.9004 (m-40)
REVERT: D   73 ILE cc_start: 0.9115 (mm) cc_final: 0.8748 (mm)
REVERT: D  113 MET cc_start: 0.7786 (pmm) cc_final: 0.7521 (pmm)
REVERT: D  115 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8566 (mmmm)
REVERT: D  119 TYR cc_start: 0.7238 (m-80) cc_final: 0.6818 (m-80)
REVERT: D  142 LEU cc_start: 0.9239 (mt) cc_final: 0.8989 (mt)
REVERT: D  145 PHE cc_start: 0.9053 (m-80) cc_final: 0.8658 (m-10)
REVERT: D  147 PHE cc_start: 0.7991 (m-10) cc_final: 0.7378 (m-80)
REVERT: D  153 ASN cc_start: 0.9099 (p0) cc_final: 0.8498 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 272
  average time/residue: 0.0533
  time to fit residues: 21.0292
Evaluate side-chains
  217 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0060
   chunk 18 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0170
   chunk 54 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 25 optimal weight:    7.9990
   chunk 16 optimal weight:   20.0000
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.121577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.098129 restraints weight = 17331.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.101692 restraints weight = 11016.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.104244 restraints weight = 7882.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.106148 restraints weight = 6119.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.107662 restraints weight = 5014.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6186  Z= 0.121
  Angle     :  0.645   7.303   8363  Z= 0.339
  Chirality :  0.044   0.162    981
  Planarity :  0.004   0.041   1006
  Dihedral  :  5.263  26.773    800
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.07 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.30), residues: 724
  helix: -0.22 (0.26), residues: 365
  sheet: -2.16 (0.63), residues: 79
  loop : -3.02 (0.32), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 151 
 TYR   0.023   0.001   TYR A 119 
 PHE   0.032   0.002   PHE A  97 
 HIS   0.001   0.000   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6186)
  covalent geometry    : angle       0.64540 ( 8363)
  hydrogen bonds       : bond        0.03413 (  263)
  hydrogen bonds       : angle       5.10314 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 277
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8781 (tpt) cc_final: 0.7494 (tpp)
REVERT: A   20 PHE cc_start: 0.9447 (m-80) cc_final: 0.9146 (m-80)
REVERT: A   22 PHE cc_start: 0.9148 (m-80) cc_final: 0.8057 (m-80)
REVERT: A   62 PHE cc_start: 0.8949 (m-10) cc_final: 0.8684 (m-10)
REVERT: A   65 TYR cc_start: 0.8261 (t80) cc_final: 0.8049 (t80)
REVERT: A   75 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8284 (mmtt)
REVERT: A  139 ASN cc_start: 0.8366 (t0) cc_final: 0.7971 (t0)
REVERT: A  141 THR cc_start: 0.9358 (m) cc_final: 0.9031 (m)
REVERT: B    1 MET cc_start: 0.5098 (tmm) cc_final: 0.4780 (tmm)
REVERT: B   77 ASN cc_start: 0.8312 (m-40) cc_final: 0.7521 (t0)
REVERT: B  128 ILE cc_start: 0.9290 (tt) cc_final: 0.8990 (tp)
REVERT: B  161 GLU cc_start: 0.7553 (tp30) cc_final: 0.6822 (tp30)
REVERT: C    5 THR cc_start: 0.8450 (p) cc_final: 0.8187 (p)
REVERT: C    6 TYR cc_start: 0.7024 (m-10) cc_final: 0.6752 (m-80)
REVERT: C   65 TYR cc_start: 0.8594 (t80) cc_final: 0.8298 (t80)
REVERT: C  112 ASP cc_start: 0.8197 (t70) cc_final: 0.7756 (t70)
REVERT: C  113 MET cc_start: 0.8141 (ptp) cc_final: 0.7526 (pmm)
REVERT: C  134 ASP cc_start: 0.9129 (t70) cc_final: 0.8582 (t0)
REVERT: C  150 TYR cc_start: 0.7394 (p90) cc_final: 0.7186 (p90)
REVERT: C  179 VAL cc_start: 0.7530 (m) cc_final: 0.7241 (m)
REVERT: D   19 LEU cc_start: 0.9483 (tt) cc_final: 0.9096 (tt)
REVERT: D   72 ASN cc_start: 0.9299 (m-40) cc_final: 0.8878 (m-40)
REVERT: D   73 ILE cc_start: 0.9019 (mm) cc_final: 0.8509 (mm)
REVERT: D  100 THR cc_start: 0.8504 (p) cc_final: 0.7942 (p)
REVERT: D  101 TYR cc_start: 0.5140 (m-10) cc_final: 0.4887 (m-10)
REVERT: D  113 MET cc_start: 0.7562 (pmm) cc_final: 0.7227 (pmm)
REVERT: D  115 LYS cc_start: 0.9298 (mmmm) cc_final: 0.8524 (mmmm)
REVERT: D  119 TYR cc_start: 0.7188 (m-80) cc_final: 0.6848 (m-80)
REVERT: D  136 TYR cc_start: 0.8260 (p90) cc_final: 0.8035 (p90)
REVERT: D  142 LEU cc_start: 0.9230 (mt) cc_final: 0.8637 (mt)
REVERT: D  145 PHE cc_start: 0.9018 (m-80) cc_final: 0.8512 (m-10)
REVERT: D  147 PHE cc_start: 0.8053 (m-10) cc_final: 0.7327 (m-80)
REVERT: D  153 ASN cc_start: 0.8984 (p0) cc_final: 0.8337 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 277
  average time/residue: 0.0584
  time to fit residues: 22.8663
Evaluate side-chains
  217 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN
C 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.119475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.096539 restraints weight = 17165.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.099759 restraints weight = 11036.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.102114 restraints weight = 8028.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.103811 restraints weight = 6302.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.105094 restraints weight = 5258.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6186  Z= 0.146
  Angle     :  0.656   7.512   8363  Z= 0.351
  Chirality :  0.044   0.185    981
  Planarity :  0.004   0.040   1006
  Dihedral  :  5.170  25.780    800
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.14 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.30), residues: 724
  helix: -0.06 (0.26), residues: 364
  sheet: -1.70 (0.60), residues: 89
  loop : -3.06 (0.33), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 151 
 TYR   0.028   0.002   TYR A 119 
 PHE   0.027   0.002   PHE A  97 
 HIS   0.001   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6186)
  covalent geometry    : angle       0.65607 ( 8363)
  hydrogen bonds       : bond        0.03520 (  263)
  hydrogen bonds       : angle       5.18574 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 271
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8660 (tpt) cc_final: 0.7480 (tpp)
REVERT: A   20 PHE cc_start: 0.9445 (m-80) cc_final: 0.9213 (m-80)
REVERT: A   22 PHE cc_start: 0.9201 (m-80) cc_final: 0.8196 (m-80)
REVERT: A   62 PHE cc_start: 0.8984 (m-10) cc_final: 0.8715 (m-10)
REVERT: A   75 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8355 (mmtt)
REVERT: A  139 ASN cc_start: 0.8501 (t0) cc_final: 0.8105 (t0)
REVERT: A  141 THR cc_start: 0.9397 (m) cc_final: 0.9071 (m)
REVERT: B    1 MET cc_start: 0.5064 (tmm) cc_final: 0.4704 (tmm)
REVERT: B   50 ASN cc_start: 0.9467 (t0) cc_final: 0.9264 (t0)
REVERT: B   77 ASN cc_start: 0.8320 (m-40) cc_final: 0.7565 (t0)
REVERT: B  128 ILE cc_start: 0.9304 (tt) cc_final: 0.9026 (tp)
REVERT: B  161 GLU cc_start: 0.7734 (tp30) cc_final: 0.6880 (tp30)
REVERT: C    6 TYR cc_start: 0.7112 (m-10) cc_final: 0.6801 (m-10)
REVERT: C   65 TYR cc_start: 0.8621 (t80) cc_final: 0.8351 (t80)
REVERT: C  112 ASP cc_start: 0.8368 (t70) cc_final: 0.7797 (t70)
REVERT: C  113 MET cc_start: 0.8153 (ptp) cc_final: 0.7525 (pmm)
REVERT: C  134 ASP cc_start: 0.9195 (t70) cc_final: 0.8602 (t0)
REVERT: C  179 VAL cc_start: 0.7552 (m) cc_final: 0.7316 (m)
REVERT: D   72 ASN cc_start: 0.9297 (m-40) cc_final: 0.9033 (m-40)
REVERT: D   73 ILE cc_start: 0.9086 (mm) cc_final: 0.8698 (mm)
REVERT: D  100 THR cc_start: 0.8567 (p) cc_final: 0.7998 (p)
REVERT: D  101 TYR cc_start: 0.5335 (m-10) cc_final: 0.4897 (m-10)
REVERT: D  113 MET cc_start: 0.7666 (pmm) cc_final: 0.7217 (pmm)
REVERT: D  114 GLN cc_start: 0.9366 (tt0) cc_final: 0.9121 (tt0)
REVERT: D  115 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8453 (mmmm)
REVERT: D  119 TYR cc_start: 0.7254 (m-80) cc_final: 0.6835 (m-80)
REVERT: D  145 PHE cc_start: 0.9015 (m-80) cc_final: 0.8607 (m-10)
REVERT: D  147 PHE cc_start: 0.8084 (m-10) cc_final: 0.7682 (m-80)
REVERT: D  153 ASN cc_start: 0.9051 (p0) cc_final: 0.8438 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 272
  average time/residue: 0.0561
  time to fit residues: 21.8796
Evaluate side-chains
  214 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:   40.0000
   chunk 58 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 48 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.120382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096981 restraints weight = 17131.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.100377 restraints weight = 10703.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.102934 restraints weight = 7672.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.104826 restraints weight = 5918.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.106255 restraints weight = 4847.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6186  Z= 0.137
  Angle     :  0.667   8.381   8363  Z= 0.350
  Chirality :  0.045   0.161    981
  Planarity :  0.004   0.039   1006
  Dihedral  :  5.221  25.232    800
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.30), residues: 724
  helix: -0.01 (0.26), residues: 363
  sheet: -1.43 (0.67), residues: 67
  loop : -3.19 (0.31), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 192 
 TYR   0.026   0.002   TYR A 119 
 PHE   0.021   0.002   PHE A  97 
 HIS   0.001   0.000   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6186)
  covalent geometry    : angle       0.66721 ( 8363)
  hydrogen bonds       : bond        0.03424 (  263)
  hydrogen bonds       : angle       5.17602 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8699 (tpt) cc_final: 0.7567 (tpp)
REVERT: A   20 PHE cc_start: 0.9478 (m-80) cc_final: 0.9236 (m-80)
REVERT: A   22 PHE cc_start: 0.9230 (m-80) cc_final: 0.8259 (m-80)
REVERT: A   62 PHE cc_start: 0.9026 (m-10) cc_final: 0.8748 (m-10)
REVERT: A   75 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8361 (mmtt)
REVERT: A  120 LEU cc_start: 0.9407 (mm) cc_final: 0.9015 (tt)
REVERT: A  139 ASN cc_start: 0.8453 (t0) cc_final: 0.8078 (t0)
REVERT: A  141 THR cc_start: 0.9407 (m) cc_final: 0.9090 (m)
REVERT: B    1 MET cc_start: 0.5130 (tmm) cc_final: 0.4737 (tmm)
REVERT: B   50 ASN cc_start: 0.9483 (t0) cc_final: 0.9268 (t0)
REVERT: B   77 ASN cc_start: 0.8311 (m-40) cc_final: 0.7438 (t0)
REVERT: B   98 LEU cc_start: 0.9135 (tt) cc_final: 0.8915 (tp)
REVERT: B  128 ILE cc_start: 0.9279 (tt) cc_final: 0.9001 (tp)
REVERT: C    5 THR cc_start: 0.8481 (p) cc_final: 0.8189 (p)
REVERT: C    6 TYR cc_start: 0.7153 (m-10) cc_final: 0.6832 (m-10)
REVERT: C   59 PHE cc_start: 0.9596 (m-80) cc_final: 0.9273 (m-80)
REVERT: C   65 TYR cc_start: 0.8648 (t80) cc_final: 0.8379 (t80)
REVERT: C   92 TYR cc_start: 0.7147 (m-10) cc_final: 0.6846 (m-10)
REVERT: C  112 ASP cc_start: 0.8431 (t70) cc_final: 0.7770 (t70)
REVERT: C  113 MET cc_start: 0.8129 (ptp) cc_final: 0.7513 (pmm)
REVERT: C  134 ASP cc_start: 0.9246 (t70) cc_final: 0.8655 (t0)
REVERT: C  179 VAL cc_start: 0.7718 (m) cc_final: 0.7391 (m)
REVERT: D   19 LEU cc_start: 0.9492 (tt) cc_final: 0.9050 (tt)
REVERT: D   72 ASN cc_start: 0.9330 (m-40) cc_final: 0.9037 (m-40)
REVERT: D   73 ILE cc_start: 0.9054 (mm) cc_final: 0.8665 (mm)
REVERT: D  113 MET cc_start: 0.7657 (pmm) cc_final: 0.7244 (pmm)
REVERT: D  114 GLN cc_start: 0.9363 (tt0) cc_final: 0.9144 (tt0)
REVERT: D  115 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8363 (mmmm)
REVERT: D  119 TYR cc_start: 0.7315 (m-80) cc_final: 0.6855 (m-80)
REVERT: D  134 ASP cc_start: 0.8976 (t70) cc_final: 0.8757 (t0)
REVERT: D  145 PHE cc_start: 0.9046 (m-80) cc_final: 0.8629 (m-10)
REVERT: D  147 PHE cc_start: 0.8247 (m-10) cc_final: 0.7869 (m-80)
REVERT: D  153 ASN cc_start: 0.9118 (p0) cc_final: 0.8535 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.0563
  time to fit residues: 21.9524
Evaluate side-chains
  217 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 32 optimal weight:   40.0000
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.119762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.096699 restraints weight = 17202.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.100181 restraints weight = 10744.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.102687 restraints weight = 7635.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.104437 restraints weight = 5894.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.105816 restraints weight = 4848.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6186  Z= 0.136
  Angle     :  0.670   7.806   8363  Z= 0.354
  Chirality :  0.045   0.186    981
  Planarity :  0.004   0.039   1006
  Dihedral  :  5.173  25.201    800
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.30), residues: 724
  helix: -0.01 (0.26), residues: 363
  sheet: -1.47 (0.67), residues: 67
  loop : -3.20 (0.31), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 192 
 TYR   0.029   0.002   TYR A 119 
 PHE   0.019   0.002   PHE D  57 
 HIS   0.001   0.000   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6186)
  covalent geometry    : angle       0.66974 ( 8363)
  hydrogen bonds       : bond        0.03388 (  263)
  hydrogen bonds       : angle       5.16465 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8689 (tpt) cc_final: 0.7548 (tpp)
REVERT: A   20 PHE cc_start: 0.9476 (m-80) cc_final: 0.9233 (m-80)
REVERT: A   22 PHE cc_start: 0.9227 (m-80) cc_final: 0.8251 (m-80)
REVERT: A   62 PHE cc_start: 0.9037 (m-10) cc_final: 0.8774 (m-10)
REVERT: A  120 LEU cc_start: 0.9420 (mm) cc_final: 0.9040 (tt)
REVERT: A  139 ASN cc_start: 0.8463 (t0) cc_final: 0.8057 (t0)
REVERT: A  141 THR cc_start: 0.9397 (m) cc_final: 0.9084 (m)
REVERT: B    1 MET cc_start: 0.5133 (tmm) cc_final: 0.4744 (tmm)
REVERT: B   45 LYS cc_start: 0.9458 (pttp) cc_final: 0.9159 (tptt)
REVERT: B   98 LEU cc_start: 0.9101 (tt) cc_final: 0.8837 (tp)
REVERT: B  128 ILE cc_start: 0.9273 (tt) cc_final: 0.8994 (tp)
REVERT: C    5 THR cc_start: 0.8475 (p) cc_final: 0.8137 (p)
REVERT: C    6 TYR cc_start: 0.7091 (m-10) cc_final: 0.6779 (m-10)
REVERT: C   59 PHE cc_start: 0.9624 (m-80) cc_final: 0.9210 (m-80)
REVERT: C   65 TYR cc_start: 0.8641 (t80) cc_final: 0.8394 (t80)
REVERT: C   92 TYR cc_start: 0.7199 (m-10) cc_final: 0.6851 (m-10)
REVERT: C  112 ASP cc_start: 0.8457 (t70) cc_final: 0.7791 (t70)
REVERT: C  113 MET cc_start: 0.8111 (ptp) cc_final: 0.7496 (pmm)
REVERT: C  134 ASP cc_start: 0.9239 (t70) cc_final: 0.8678 (t0)
REVERT: C  150 TYR cc_start: 0.7659 (p90) cc_final: 0.7373 (p90)
REVERT: C  154 ILE cc_start: 0.9165 (pt) cc_final: 0.8965 (pt)
REVERT: C  179 VAL cc_start: 0.7803 (m) cc_final: 0.7474 (m)
REVERT: D   19 LEU cc_start: 0.9476 (tt) cc_final: 0.9043 (tt)
REVERT: D   72 ASN cc_start: 0.9332 (m-40) cc_final: 0.9083 (m-40)
REVERT: D   73 ILE cc_start: 0.9066 (mm) cc_final: 0.8663 (mm)
REVERT: D  113 MET cc_start: 0.7645 (pmm) cc_final: 0.7225 (pmm)
REVERT: D  114 GLN cc_start: 0.9375 (tt0) cc_final: 0.9159 (tt0)
REVERT: D  115 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8348 (mmmm)
REVERT: D  119 TYR cc_start: 0.7379 (m-80) cc_final: 0.6921 (m-80)
REVERT: D  147 PHE cc_start: 0.8304 (m-10) cc_final: 0.7953 (m-80)
REVERT: D  153 ASN cc_start: 0.9137 (p0) cc_final: 0.8593 (p0)
REVERT: D  163 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8669 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.0571
  time to fit residues: 21.4308
Evaluate side-chains
  221 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.121318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.097847 restraints weight = 17403.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.101467 restraints weight = 10902.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.104021 restraints weight = 7739.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.105674 restraints weight = 5957.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.107160 restraints weight = 4943.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6186  Z= 0.129
  Angle     :  0.672   7.770   8363  Z= 0.352
  Chirality :  0.045   0.182    981
  Planarity :  0.004   0.038   1006
  Dihedral  :  5.156  24.767    800
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.30), residues: 724
  helix: -0.02 (0.26), residues: 369
  sheet: -1.18 (0.65), residues: 77
  loop : -3.37 (0.31), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 192 
 TYR   0.028   0.001   TYR A 119 
 PHE   0.026   0.002   PHE D  62 
 HIS   0.001   0.000   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6186)
  covalent geometry    : angle       0.67160 ( 8363)
  hydrogen bonds       : bond        0.03328 (  263)
  hydrogen bonds       : angle       5.16929 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8711 (tpt) cc_final: 0.7511 (tpp)
REVERT: A   22 PHE cc_start: 0.9217 (m-80) cc_final: 0.8263 (m-80)
REVERT: A   62 PHE cc_start: 0.9052 (m-10) cc_final: 0.8774 (m-10)
REVERT: A   65 TYR cc_start: 0.8294 (t80) cc_final: 0.8087 (t80)
REVERT: A  120 LEU cc_start: 0.9407 (mm) cc_final: 0.9015 (tt)
REVERT: A  139 ASN cc_start: 0.8439 (t0) cc_final: 0.8041 (t0)
REVERT: A  141 THR cc_start: 0.9370 (m) cc_final: 0.9062 (m)
REVERT: B    1 MET cc_start: 0.5127 (tmm) cc_final: 0.4762 (tmm)
REVERT: B   77 ASN cc_start: 0.8221 (m-40) cc_final: 0.7491 (t0)
REVERT: B   98 LEU cc_start: 0.9021 (tt) cc_final: 0.8769 (tp)
REVERT: B  128 ILE cc_start: 0.9293 (tt) cc_final: 0.9015 (tp)
REVERT: B  161 GLU cc_start: 0.7571 (tp30) cc_final: 0.6771 (tp30)
REVERT: C    5 THR cc_start: 0.8524 (p) cc_final: 0.8256 (p)
REVERT: C    6 TYR cc_start: 0.7115 (m-10) cc_final: 0.6800 (m-10)
REVERT: C   59 PHE cc_start: 0.9620 (m-80) cc_final: 0.9121 (m-80)
REVERT: C   65 TYR cc_start: 0.8630 (t80) cc_final: 0.8382 (t80)
REVERT: C   92 TYR cc_start: 0.7184 (m-10) cc_final: 0.6888 (m-10)
REVERT: C  112 ASP cc_start: 0.8438 (t70) cc_final: 0.7802 (t70)
REVERT: C  113 MET cc_start: 0.8228 (ptp) cc_final: 0.7550 (pmm)
REVERT: C  134 ASP cc_start: 0.9248 (t70) cc_final: 0.8684 (t0)
REVERT: C  150 TYR cc_start: 0.7659 (p90) cc_final: 0.7363 (p90)
REVERT: C  154 ILE cc_start: 0.9164 (pt) cc_final: 0.8951 (pt)
REVERT: C  179 VAL cc_start: 0.7754 (m) cc_final: 0.7421 (m)
REVERT: D   19 LEU cc_start: 0.9496 (tt) cc_final: 0.9140 (tt)
REVERT: D   72 ASN cc_start: 0.9371 (m-40) cc_final: 0.9104 (m-40)
REVERT: D   73 ILE cc_start: 0.9061 (mm) cc_final: 0.8652 (mm)
REVERT: D  113 MET cc_start: 0.7684 (pmm) cc_final: 0.7231 (pmm)
REVERT: D  114 GLN cc_start: 0.9362 (tt0) cc_final: 0.9157 (tt0)
REVERT: D  115 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8347 (mmmm)
REVERT: D  119 TYR cc_start: 0.7341 (m-80) cc_final: 0.6870 (m-80)
REVERT: D  147 PHE cc_start: 0.8264 (m-10) cc_final: 0.7920 (m-80)
REVERT: D  153 ASN cc_start: 0.9096 (p0) cc_final: 0.8542 (p0)
REVERT: D  163 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8665 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.0563
  time to fit residues: 22.7045
Evaluate side-chains
  217 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 11 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0030
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.122558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.099108 restraints weight = 17001.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.102630 restraints weight = 10650.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.105187 restraints weight = 7586.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.107049 restraints weight = 5857.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.108546 restraints weight = 4798.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6186  Z= 0.125
  Angle     :  0.674   7.609   8363  Z= 0.352
  Chirality :  0.045   0.162    981
  Planarity :  0.003   0.039   1006
  Dihedral  :  5.086  25.013    800
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.30), residues: 724
  helix:  0.05 (0.26), residues: 367
  sheet: -1.11 (0.64), residues: 79
  loop : -3.37 (0.31), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 192 
 TYR   0.034   0.002   TYR B  76 
 PHE   0.020   0.002   PHE B  66 
 HIS   0.001   0.000   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6186)
  covalent geometry    : angle       0.67429 ( 8363)
  hydrogen bonds       : bond        0.03268 (  263)
  hydrogen bonds       : angle       5.12328 (  747)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8683 (tpt) cc_final: 0.7474 (tpp)
REVERT: A   22 PHE cc_start: 0.9164 (m-80) cc_final: 0.8141 (m-80)
REVERT: A   26 LEU cc_start: 0.8640 (tp) cc_final: 0.8362 (tt)
REVERT: A   62 PHE cc_start: 0.8970 (m-10) cc_final: 0.8702 (m-10)
REVERT: A  120 LEU cc_start: 0.9383 (mm) cc_final: 0.8981 (tt)
REVERT: A  139 ASN cc_start: 0.8408 (t0) cc_final: 0.8025 (t0)
REVERT: A  141 THR cc_start: 0.9356 (m) cc_final: 0.9038 (m)
REVERT: B    1 MET cc_start: 0.5083 (tmm) cc_final: 0.4720 (tmm)
REVERT: B   16 LEU cc_start: 0.9336 (mt) cc_final: 0.9076 (tt)
REVERT: B   50 ASN cc_start: 0.9425 (t0) cc_final: 0.9218 (t0)
REVERT: B   77 ASN cc_start: 0.8233 (m-40) cc_final: 0.7510 (t0)
REVERT: B   98 LEU cc_start: 0.9042 (tt) cc_final: 0.8770 (tp)
REVERT: B  128 ILE cc_start: 0.9290 (tt) cc_final: 0.8994 (tp)
REVERT: B  161 GLU cc_start: 0.7498 (tp30) cc_final: 0.6564 (tp30)
REVERT: C    5 THR cc_start: 0.8506 (p) cc_final: 0.8255 (p)
REVERT: C    6 TYR cc_start: 0.7150 (m-10) cc_final: 0.6800 (m-10)
REVERT: C   59 PHE cc_start: 0.9548 (m-80) cc_final: 0.9086 (m-80)
REVERT: C   65 TYR cc_start: 0.8560 (t80) cc_final: 0.8283 (t80)
REVERT: C   92 TYR cc_start: 0.7104 (m-10) cc_final: 0.6816 (m-10)
REVERT: C  112 ASP cc_start: 0.8237 (t70) cc_final: 0.7604 (t70)
REVERT: C  113 MET cc_start: 0.8212 (ptp) cc_final: 0.7510 (pmm)
REVERT: C  134 ASP cc_start: 0.9198 (t70) cc_final: 0.8650 (t0)
REVERT: C  150 TYR cc_start: 0.7606 (p90) cc_final: 0.7345 (p90)
REVERT: C  179 VAL cc_start: 0.7702 (m) cc_final: 0.7372 (m)
REVERT: D   19 LEU cc_start: 0.9496 (tt) cc_final: 0.9172 (tt)
REVERT: D   72 ASN cc_start: 0.9345 (m-40) cc_final: 0.8497 (t0)
REVERT: D   73 ILE cc_start: 0.9053 (mm) cc_final: 0.8502 (mm)
REVERT: D   76 TYR cc_start: 0.7978 (m-80) cc_final: 0.7761 (m-10)
REVERT: D  113 MET cc_start: 0.7662 (pmm) cc_final: 0.7200 (pmm)
REVERT: D  114 GLN cc_start: 0.9360 (tt0) cc_final: 0.9146 (tt0)
REVERT: D  115 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8340 (mmmm)
REVERT: D  119 TYR cc_start: 0.7314 (m-80) cc_final: 0.6867 (m-80)
REVERT: D  147 PHE cc_start: 0.8264 (m-10) cc_final: 0.7921 (m-80)
REVERT: D  153 ASN cc_start: 0.9043 (p0) cc_final: 0.8456 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 282
  average time/residue: 0.0555
  time to fit residues: 22.2886
Evaluate side-chains
  212 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 24 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.116588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.093227 restraints weight = 18526.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.096474 restraints weight = 12151.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.098748 restraints weight = 8910.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.100513 restraints weight = 7098.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.101661 restraints weight = 5936.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6186  Z= 0.173
  Angle     :  0.722   7.837   8363  Z= 0.381
  Chirality :  0.045   0.169    981
  Planarity :  0.004   0.036   1006
  Dihedral  :  5.181  24.643    800
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.30), residues: 724
  helix: -0.00 (0.26), residues: 369
  sheet: -1.49 (0.58), residues: 99
  loop : -3.34 (0.33), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 192 
 TYR   0.035   0.002   TYR A 119 
 PHE   0.028   0.002   PHE C  60 
 HIS   0.001   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6186)
  covalent geometry    : angle       0.72178 ( 8363)
  hydrogen bonds       : bond        0.03559 (  263)
  hydrogen bonds       : angle       5.27021 (  747)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1157.30 seconds
wall clock time: 20 minutes 43.17 seconds (1243.17 seconds total)