Starting phenix.real_space_refine
on Sat May  2 13:57:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qpe_53274/05_2026/9qpe_53274.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qpe_53274/05_2026/9qpe_53274.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qpe_53274/05_2026/9qpe_53274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qpe_53274/05_2026/9qpe_53274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qpe_53274/05_2026/9qpe_53274.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qpe_53274/05_2026/9qpe_53274.cif"
  }
  resolution = 3.8
  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=   0.082
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      34      5.16       5
     C    3885      2.51       5
     N     969      2.21       5
     O    1183      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6071
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 867
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 867
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 794
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
          Chain breaks: 5
    Chain: "D"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 703
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
          Chain breaks: 6
    Chain: "E"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 723
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
          Chain breaks: 5
    Chain: "F"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 775
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
          Chain breaks: 5
    Chain: "G"
      Number of atoms: 1342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1342
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 4, 'TRANS': 173}
          Chain breaks: 6
  Time building chain proxies: 1.50, per 1000 atoms: 0.25
  Number of scatterers: 6071
  At special positions: 0
  Unit cell: (66.312, 100.389, 96.705, 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      34     16.00
     O    1183      8.00
     N     969      7.00
     C    3885      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: 0.49
  Conformation dependent library (CDL) restraints added in 316.6 milliseconds
  

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1476

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 12 sheets defined
      14.0% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 73
      removed outlier: 4.624A  pdb=" N   THR A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   TYR A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 75
      removed outlier: 3.549A  pdb=" N   LEU B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ASN B  71 " --> pdb=" O   THR B  67 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLU B  72 " --> pdb=" O   PRO B  68 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS B  75 " --> pdb=" O   ASN B  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 75
      removed outlier: 3.695A  pdb=" N   ASN C  71 " --> pdb=" O   THR C  67 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLU C  72 " --> pdb=" O   PRO C  68 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   TYR C  73 " --> pdb=" O   THR C  69 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   CYS C  74 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 75
      removed outlier: 3.612A  pdb=" N   LEU D  70 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS D  74 " --> pdb=" O   LEU D  70 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 74
      removed outlier: 3.906A  pdb=" N   LEU E  70 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASN E  71 " --> pdb=" O   THR E  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 74
    Processing helix  chain 'G' and resid 129 through 140
    Processing helix  chain 'G' and resid 157 through 171
    Processing helix  chain 'G' and resid 217 through 229
    Processing helix  chain 'G' and resid 245 through 259
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 4.388A  pdb=" N   ILE A   4 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA A   3 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLY A  88 " --> pdb=" O   ALA A   3 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ILE A  85 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   VAL A 103 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE A  87 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 35
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 57 through 61
    current: chain 'A' and resid 125 through 131
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 125 through 131
    current: chain 'B' and resid 56 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 56 through 61
    current: chain 'B' and resid 125 through 131
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 125 through 131
    current: chain 'C' and resid 25 through 27
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 25 through 27
    current: chain 'C' and resid 57 through 62
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 57 through 62
    current: chain 'C' and resid 99 through 119
      removed outlier: 5.507A  pdb=" N   LEU C 111 " --> pdb=" O   ASN C 131 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASN C 131 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ASN C 113 " --> pdb=" O   SER C 129 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   GLY C 119 " --> pdb=" O   LYS C 123 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   LYS C 123 " --> pdb=" O   GLY C 119 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 122 through 131
    current: chain 'D' and resid 57 through 62
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 57 through 62
    current: chain 'D' and resid 125 through 130
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 125 through 130
    current: chain 'E' and resid 57 through 62
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 57 through 62
    current: chain 'E' and resid 125 through 130
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 125 through 130
    current: chain 'F' and resid 57 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 57 through 61
    current: chain 'F' and resid 122 through 130
    Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107
      removed outlier: 3.800A  pdb=" N   LYS A 134 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 27
      removed outlier: 3.758A  pdb=" N   ILE B   4 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ALA B   3 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASP B   7 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   THR B  84 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE B  85 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   VAL B 103 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE B  87 " --> pdb=" O   PHE B 101 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 107
      removed outlier: 3.883A  pdb=" N   LYS B 134 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 25 through 27
      removed outlier: 3.627A  pdb=" N   ILE D  27 " --> pdb=" O   ILE D   4 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ILE D   4 " --> pdb=" O   ILE D  27 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ARG D  89 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 25 through 26
    Processing sheet with id=AA8, first strand: chain 'F' and resid 25 through 27
      removed outlier: 3.947A  pdb=" N   ILE F   4 " --> pdb=" O   ILE F  27 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ILE F  85 " --> pdb=" O   TYR F 104 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR F 104 " --> pdb=" O   ILE F  85 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 113 through 114
    Processing sheet with id=AB1, first strand: chain 'G' and resid 116 through 117
      removed outlier: 3.665A  pdb=" N   TYR G 117 " --> pdb=" O   ILE G 152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'G' and resid 234 through 235
      removed outlier: 3.527A  pdb=" N   TYR G 265 " --> pdb=" O   ILE G 235 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA G 266 " --> pdb=" O   VAL G 290 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA G 288 " --> pdb=" O   LYS G 268 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU G 300 " --> pdb=" O   MET G 289 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 271 through 273
      removed outlier: 4.181A  pdb=" N   TYR G 272 " --> pdb=" O   THR G 284 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   THR G 284 " --> pdb=" O   TYR G 272 " (cutoff:3.500A)

    150 hydrogen bonds defined for protein.
    393 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.67 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: 1893
        1.34 -     1.46: 1234
        1.46 -     1.58: 2958
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 6141
  Sorted by residual:
  bond pdb=" CA  TYR B 104 "
       pdb=" C   TYR B 104 "
    ideal  model  delta    sigma   weight residual
    1.528  1.478  0.050 1.51e-02 4.39e+03 1.11e+01
  bond pdb=" N   TYR B 104 "
       pdb=" CA  TYR B 104 "
    ideal  model  delta    sigma   weight residual
    1.453  1.477 -0.024 1.39e-02 5.18e+03 3.07e+00
  bond pdb=" N   LYS A 123 "
       pdb=" CA  LYS A 123 "
    ideal  model  delta    sigma   weight residual
    1.453  1.477 -0.024 1.44e-02 4.82e+03 2.80e+00
  bond pdb=" CA  TYR G 265 "
       pdb=" CB  TYR G 265 "
    ideal  model  delta    sigma   weight residual
    1.526  1.509  0.017 1.49e-02 4.50e+03 1.25e+00
  bond pdb=" CA  VAL G 290 "
       pdb=" CB  VAL G 290 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.05e-02 9.07e+03 1.21e+00
  ... (remaining 6136 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 8025
        1.72 -     3.45: 206
        3.45 -     5.17: 31
        5.17 -     6.90: 5
        6.90 -     8.62: 6
  Bond angle restraints: 8273
  Sorted by residual:
  angle pdb=" N   TYR B 104 "
        pdb=" CA  TYR B 104 "
        pdb=" CB  TYR B 104 "
      ideal   model   delta    sigma   weight residual
     110.14  117.98   -7.84 1.72e+00 3.38e-01 2.08e+01
  angle pdb=" C   TYR B 104 "
        pdb=" CA  TYR B 104 "
        pdb=" CB  TYR B 104 "
      ideal   model   delta    sigma   weight residual
     112.43  103.81    8.62 1.91e+00 2.74e-01 2.04e+01
  angle pdb=" N   GLY C  88 "
        pdb=" CA  GLY C  88 "
        pdb=" C   GLY C  88 "
      ideal   model   delta    sigma   weight residual
     111.18  117.22   -6.04 1.54e+00 4.22e-01 1.54e+01
  angle pdb=" CA  GLY A 118 "
        pdb=" C   GLY A 118 "
        pdb=" N   GLY A 119 "
      ideal   model   delta    sigma   weight residual
     114.23  117.25   -3.02 8.80e-01 1.29e+00 1.18e+01
  angle pdb=" C   VAL B 103 "
        pdb=" N   TYR B 104 "
        pdb=" CA  TYR B 104 "
      ideal   model   delta    sigma   weight residual
     123.20  116.30    6.90 2.05e+00 2.38e-01 1.13e+01
  ... (remaining 8268 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 3287
       15.94 -    31.87: 271
       31.87 -    47.81: 44
       47.81 -    63.75: 21
       63.75 -    79.68: 8
  Dihedral angle restraints: 3631
    sinusoidal: 1374
      harmonic: 2257
  Sorted by residual:
  dihedral pdb=" CA  ARG G 126 "
           pdb=" C   ARG G 126 "
           pdb=" N   GLY G 127 "
           pdb=" CA  GLY G 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.67  -28.33     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  ASP G 119 "
           pdb=" C   ASP G 119 "
           pdb=" N   PHE G 120 "
           pdb=" CA  PHE G 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.80   20.20     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  TYR G 117 "
           pdb=" C   TYR G 117 "
           pdb=" N   HIS G 118 "
           pdb=" CA  HIS G 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 3628 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 637
       0.034 -    0.069: 212
       0.069 -    0.103: 99
       0.103 -    0.137: 52
       0.137 -    0.171: 12
  Chirality restraints: 1012
  Sorted by residual:
  chirality pdb=" CA  ILE A  87 "
            pdb=" N   ILE A  87 "
            pdb=" C   ILE A  87 "
            pdb=" CB  ILE A  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.34e-01
  chirality pdb=" CB  ILE D   4 "
            pdb=" CA  ILE D   4 "
            pdb=" CG1 ILE D   4 "
            pdb=" CG2 ILE D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.02e-01
  chirality pdb=" CA  ILE F  87 "
            pdb=" N   ILE F  87 "
            pdb=" C   ILE F  87 "
            pdb=" CB  ILE F  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.89e-01
  ... (remaining 1009 not shown)

  Planarity restraints: 1010
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 103 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.02e+00
        pdb=" C   VAL B 103 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   VAL B 103 "    0.009 2.00e-02 2.50e+03
        pdb=" N   TYR B 104 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G 120 "    0.011 2.00e-02 2.50e+03   1.06e-02 1.97e+00
        pdb=" CG  PHE G 120 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE G 120 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE G 120 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE G 120 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE G 120 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE G 120 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 104 "    0.014 2.00e-02 2.50e+03   9.89e-03 1.96e+00
        pdb=" CG  TYR C 104 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 104 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 104 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 104 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 104 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 104 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C 104 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1007 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 513
        2.74 -     3.28: 5947
        3.28 -     3.82: 9611
        3.82 -     4.36: 10853
        4.36 -     4.90: 19703
  Nonbonded interactions: 46627
  Sorted by model distance:
  nonbonded pdb=" OG  SER E  31 "
            pdb=" OG1 THR E  58 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OH  TYR B  30 "
            pdb=" OH  TYR B 104 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD1 ASN D  33 "
            pdb=" OG  SER E 115 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   SER A  16 "
            pdb=" N   ASN A  23 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" OG  SER A  16 "
            pdb=" N   LYS A  24 "
     model   vdw
     2.314 3.120
  ... (remaining 46622 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 8 or resid 11 through 34 or resid 56 through 90  \ 
or resid 98 through 141))
  selection = (chain 'B' and (resid 1 through 8 or resid 11 through 34 or resid 56 through 90  \ 
or resid 98 through 141))
  selection = (chain 'C' and (resid 1 through 90 or resid 98 through 141))
}
ncs_group {
  reference = (chain 'D' and (resid 3 through 74 or resid 82 through 89 or resid 100 through 1 \ 
39))
  selection = (chain 'E' and (resid 3 through 8 or resid 12 through 33 or resid 56 through 74  \ 
or resid 82 through 89 or resid 100 through 107 or resid 114 through 139))
  selection = (chain 'F' and (resid 3 through 8 or resid 12 through 16 or resid 23 through 33  \ 
or resid 56 through 89 or resid 100 through 106 or resid 113 through 139))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.960
  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:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.560
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5384
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6141  Z= 0.192
  Angle     :  0.711   8.620   8273  Z= 0.389
  Chirality :  0.049   0.171   1012
  Planarity :  0.003   0.031   1010
  Dihedral  : 13.378  79.681   2155
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.00 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.32), residues: 711
  helix:  0.16 (0.56), residues: 94
  sheet: -0.21 (0.34), residues: 262
  loop : -1.89 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  89 
 TYR   0.024   0.002   TYR C 104 
 PHE   0.023   0.002   PHE G 120 
 TRP   0.009   0.001   TRP D 137 
 HIS   0.003   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 6141)
  covalent geometry    : angle       0.71068 ( 8273)
  hydrogen bonds       : bond        0.18184 (  150)
  hydrogen bonds       : angle       8.01160 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: B  104 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.5360 (m-80)
REVERT: B  137 TRP cc_start: 0.5588 (m100) cc_final: 0.5175 (m100)
REVERT: C   99 MET cc_start: 0.4815 (ptp) cc_final: 0.4535 (ptp)
REVERT: E   36 MET cc_start: 0.0186 (ptp) cc_final: -0.0500 (pmm)
REVERT: E  123 LYS cc_start: 0.6914 (tptt) cc_final: 0.6455 (tptt)
REVERT: F    1 MET cc_start: 0.5139 (mmp) cc_final: 0.4582 (mtp)
REVERT: G  163 ARG cc_start: 0.7658 (ttt180) cc_final: 0.7301 (ttp80)
REVERT: G  289 MET cc_start: 0.7364 (ppp) cc_final: 0.6728 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0779
  time to fit residues: 14.6829
Evaluate side-chains
  117 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  104 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
D  33 ASN
G 186 HIS
** G 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.210199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.161573 restraints weight = 5359.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.165666 restraints weight = 6427.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.166535 restraints weight = 5548.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.171343 restraints weight = 3641.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.171296 restraints weight = 2585.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6086
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   6141  Z= 0.252
  Angle     :  0.731   9.458   8273  Z= 0.376
  Chirality :  0.052   0.224   1012
  Planarity :  0.004   0.033   1010
  Dihedral  :  5.817  29.170    798
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.13 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  9.99 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.32), residues: 711
  helix: -0.26 (0.53), residues: 95
  sheet: -0.61 (0.33), residues: 266
  loop : -2.07 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG G 125 
 TYR   0.030   0.003   TYR A 104 
 PHE   0.022   0.003   PHE G 120 
 TRP   0.009   0.002   TRP E 137 
 HIS   0.005   0.001   HIS G 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 6141)
  covalent geometry    : angle       0.73108 ( 8273)
  hydrogen bonds       : bond        0.04766 (  150)
  hydrogen bonds       : angle       6.93473 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.219 
Fit side-chains
REVERT: B   24 LYS cc_start: 0.4476 (mttt) cc_final: 0.3237 (tttt)
REVERT: C   99 MET cc_start: 0.5223 (ptp) cc_final: 0.4890 (ptp)
REVERT: E   36 MET cc_start: 0.0484 (ptp) cc_final: -0.0229 (pmm)
REVERT: F   70 LEU cc_start: 0.7510 (mt) cc_final: 0.7241 (mt)
REVERT: F  106 LEU cc_start: 0.7827 (mt) cc_final: 0.7604 (mp)
REVERT: G  125 ARG cc_start: 0.7013 (tpp80) cc_final: 0.6593 (tpt170)
REVERT: G  289 MET cc_start: 0.7895 (ppp) cc_final: 0.7263 (ppp)
  outliers start: 17
  outliers final: 15
  residues processed: 125
  average time/residue: 0.0792
  time to fit residues: 13.2583
Evaluate side-chains
  128 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain D residue  125 VAL
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  113 VAL
Chi-restraints excluded: chain G residue  205 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0070
   chunk 7 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.217148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.169854 restraints weight = 5173.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.172976 restraints weight = 5694.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.174142 restraints weight = 5081.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.177533 restraints weight = 3412.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.177975 restraints weight = 2682.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5999
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6141  Z= 0.131
  Angle     :  0.580   7.403   8273  Z= 0.295
  Chirality :  0.048   0.151   1012
  Planarity :  0.003   0.037   1010
  Dihedral  :  4.935  26.863    796
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.05 %
    Favored  : 82.41 %
  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 are not related in a simple way.
  whole: -1.46 (0.32), residues: 711
  helix:  0.03 (0.55), residues: 97
  sheet: -0.26 (0.34), residues: 263
  loop : -1.83 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.018   0.002   TYR G 292 
 PHE   0.010   0.001   PHE G 242 
 TRP   0.009   0.001   TRP E 137 
 HIS   0.003   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6141)
  covalent geometry    : angle       0.58007 ( 8273)
  hydrogen bonds       : bond        0.03606 (  150)
  hydrogen bonds       : angle       6.25196 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.198 
Fit side-chains
REVERT: B   24 LYS cc_start: 0.4241 (mttt) cc_final: 0.3030 (tttt)
REVERT: B  137 TRP cc_start: 0.6277 (OUTLIER) cc_final: 0.5832 (m-90)
REVERT: C   99 MET cc_start: 0.5235 (ptp) cc_final: 0.4876 (ptp)
REVERT: D   89 ARG cc_start: 0.3573 (mmt180) cc_final: 0.3304 (mmt180)
REVERT: E   36 MET cc_start: 0.0862 (ptp) cc_final: -0.0135 (pmm)
REVERT: F   70 LEU cc_start: 0.7415 (mt) cc_final: 0.7127 (mt)
REVERT: F  104 TYR cc_start: 0.8465 (m-80) cc_final: 0.8073 (m-80)
REVERT: F  106 LEU cc_start: 0.7827 (mt) cc_final: 0.7560 (mp)
  outliers start: 17
  outliers final: 11
  residues processed: 132
  average time/residue: 0.0745
  time to fit residues: 13.2890
Evaluate side-chains
  125 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.217256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.169995 restraints weight = 5204.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.171628 restraints weight = 5817.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.173325 restraints weight = 5440.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.175952 restraints weight = 3676.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.176947 restraints weight = 3094.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6038
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6141  Z= 0.132
  Angle     :  0.571   7.730   8273  Z= 0.291
  Chirality :  0.048   0.149   1012
  Planarity :  0.003   0.040   1010
  Dihedral  :  4.832  26.256    796
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.84 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.32), residues: 711
  helix:  0.08 (0.55), residues: 97
  sheet: -0.26 (0.35), residues: 259
  loop : -1.72 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  89 
 TYR   0.016   0.002   TYR G 292 
 PHE   0.010   0.001   PHE G 242 
 TRP   0.013   0.001   TRP C 137 
 HIS   0.003   0.001   HIS G 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6141)
  covalent geometry    : angle       0.57068 ( 8273)
  hydrogen bonds       : bond        0.03470 (  150)
  hydrogen bonds       : angle       6.00200 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.4111 (mttt) cc_final: 0.2871 (tttt)
REVERT: B  137 TRP cc_start: 0.6206 (OUTLIER) cc_final: 0.5841 (m-90)
REVERT: C   99 MET cc_start: 0.5258 (ptp) cc_final: 0.4933 (ptp)
REVERT: E   36 MET cc_start: 0.0872 (ptp) cc_final: -0.0504 (pmm)
REVERT: F   70 LEU cc_start: 0.7370 (mt) cc_final: 0.7100 (mt)
REVERT: F  106 LEU cc_start: 0.7803 (mt) cc_final: 0.7528 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0743
  time to fit residues: 13.4390
Evaluate side-chains
  133 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain G residue  129 SER
Chi-restraints excluded: chain G residue  205 VAL
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Chi-restraints excluded: chain G residue  290 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0170
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0040
   overall best weight:    0.5030

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.221463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.172995 restraints weight = 5235.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.176064 restraints weight = 4897.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.179214 restraints weight = 4070.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.180365 restraints weight = 2957.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.181648 restraints weight = 2679.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6141  Z= 0.112
  Angle     :  0.551   8.486   8273  Z= 0.278
  Chirality :  0.047   0.151   1012
  Planarity :  0.003   0.041   1010
  Dihedral  :  4.535  25.182    796
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.93 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.32), residues: 711
  helix:  0.11 (0.55), residues: 99
  sheet: -0.11 (0.34), residues: 261
  loop : -1.74 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  89 
 TYR   0.015   0.001   TYR G 292 
 PHE   0.011   0.001   PHE G 120 
 TRP   0.013   0.001   TRP C 137 
 HIS   0.003   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6141)
  covalent geometry    : angle       0.55120 ( 8273)
  hydrogen bonds       : bond        0.03119 (  150)
  hydrogen bonds       : angle       5.75245 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  123 LYS cc_start: 0.7781 (tttp) cc_final: 0.7525 (ttpp)
REVERT: B   24 LYS cc_start: 0.4036 (mttt) cc_final: 0.2874 (tttt)
REVERT: B  137 TRP cc_start: 0.6109 (OUTLIER) cc_final: 0.5761 (m-90)
REVERT: C    1 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7192 (ppp)
REVERT: C   99 MET cc_start: 0.5392 (ptp) cc_final: 0.5011 (ptp)
REVERT: D   89 ARG cc_start: 0.3476 (mmt180) cc_final: 0.3008 (mmt180)
REVERT: E   36 MET cc_start: 0.1073 (ptp) cc_final: -0.0196 (pmm)
REVERT: F   70 LEU cc_start: 0.7389 (mt) cc_final: 0.7121 (mt)
REVERT: F  106 LEU cc_start: 0.7799 (mt) cc_final: 0.7473 (mp)
REVERT: G  289 MET cc_start: 0.7775 (ppp) cc_final: 0.7281 (ppp)
  outliers start: 25
  outliers final: 19
  residues processed: 132
  average time/residue: 0.0721
  time to fit residues: 13.1095
Evaluate side-chains
  133 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  113 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain G residue  186 HIS
Chi-restraints excluded: chain G residue  257 ILE
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Chi-restraints excluded: chain G residue  290 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.216590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.168923 restraints weight = 5292.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.170389 restraints weight = 4891.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.172437 restraints weight = 4377.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.173262 restraints weight = 3090.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.174106 restraints weight = 3193.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6057
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6141  Z= 0.150
  Angle     :  0.591   9.021   8273  Z= 0.298
  Chirality :  0.047   0.152   1012
  Planarity :  0.003   0.040   1010
  Dihedral  :  4.753  25.803    796
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 18.63 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.33), residues: 711
  helix:  0.02 (0.56), residues: 98
  sheet: -0.33 (0.33), residues: 269
  loop : -1.68 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.020   0.002   TYR A 104 
 PHE   0.012   0.001   PHE G 120 
 TRP   0.012   0.001   TRP C 137 
 HIS   0.004   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6141)
  covalent geometry    : angle       0.59064 ( 8273)
  hydrogen bonds       : bond        0.03404 (  150)
  hydrogen bonds       : angle       5.89403 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 113
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   82 GLU cc_start: 0.7039 (pm20) cc_final: 0.6796 (pm20)
REVERT: B   24 LYS cc_start: 0.3937 (mttt) cc_final: 0.2818 (tttt)
REVERT: B   28 MET cc_start: 0.6397 (ptp) cc_final: 0.6155 (ptp)
REVERT: B  137 TRP cc_start: 0.6131 (OUTLIER) cc_final: 0.5724 (m-90)
REVERT: C   99 MET cc_start: 0.5359 (ptp) cc_final: 0.4998 (ptp)
REVERT: D   89 ARG cc_start: 0.3784 (mmt180) cc_final: 0.3287 (mmt180)
REVERT: E   36 MET cc_start: 0.0940 (ptp) cc_final: -0.0223 (pmm)
REVERT: E  123 LYS cc_start: 0.7389 (tptt) cc_final: 0.7173 (tptt)
REVERT: F   70 LEU cc_start: 0.7371 (mt) cc_final: 0.7110 (mt)
REVERT: F  106 LEU cc_start: 0.7863 (mt) cc_final: 0.7565 (mp)
  outliers start: 35
  outliers final: 27
  residues processed: 133
  average time/residue: 0.0695
  time to fit residues: 12.6166
Evaluate side-chains
  136 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  113 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain G residue  180 THR
Chi-restraints excluded: chain G residue  186 HIS
Chi-restraints excluded: chain G residue  205 VAL
Chi-restraints excluded: chain G residue  257 ILE
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Chi-restraints excluded: chain G residue  290 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 35 optimal weight:    0.1980
   chunk 41 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0770
   chunk 53 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.220046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.171189 restraints weight = 5226.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.172800 restraints weight = 4807.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.175013 restraints weight = 4268.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.175948 restraints weight = 3030.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.176824 restraints weight = 3095.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6065
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6141  Z= 0.117
  Angle     :  0.560  10.077   8273  Z= 0.280
  Chirality :  0.047   0.150   1012
  Planarity :  0.003   0.039   1010
  Dihedral  :  4.503  24.796    796
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.52 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.33), residues: 711
  helix:  0.15 (0.55), residues: 99
  sheet: -0.21 (0.34), residues: 262
  loop : -1.66 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  89 
 TYR   0.015   0.001   TYR A 104 
 PHE   0.011   0.001   PHE G 120 
 TRP   0.013   0.001   TRP C 137 
 HIS   0.004   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6141)
  covalent geometry    : angle       0.56031 ( 8273)
  hydrogen bonds       : bond        0.03039 (  150)
  hydrogen bonds       : angle       5.62876 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.3874 (mttt) cc_final: 0.2725 (tttt)
REVERT: B   31 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.7935 (m)
REVERT: B  137 TRP cc_start: 0.6178 (OUTLIER) cc_final: 0.5795 (m-90)
REVERT: C   99 MET cc_start: 0.5450 (ptp) cc_final: 0.5106 (ptp)
REVERT: D   89 ARG cc_start: 0.3723 (mmt180) cc_final: 0.3194 (mmt180)
REVERT: E   36 MET cc_start: 0.1102 (ptp) cc_final: -0.0092 (pmm)
REVERT: F   70 LEU cc_start: 0.7331 (mt) cc_final: 0.7053 (mt)
REVERT: F  106 LEU cc_start: 0.7814 (mt) cc_final: 0.7500 (mp)
REVERT: G  289 MET cc_start: 0.7696 (ppp) cc_final: 0.7134 (ppp)
  outliers start: 31
  outliers final: 26
  residues processed: 133
  average time/residue: 0.0731
  time to fit residues: 13.3546
Evaluate side-chains
  138 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  113 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain G residue  186 HIS
Chi-restraints excluded: chain G residue  205 VAL
Chi-restraints excluded: chain G residue  257 ILE
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Chi-restraints excluded: chain G residue  290 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 28 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** G 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.212080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.166225 restraints weight = 5367.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.167734 restraints weight = 5914.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.169523 restraints weight = 5614.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.171208 restraints weight = 3796.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.172389 restraints weight = 3456.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6156
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6141  Z= 0.185
  Angle     :  0.646  10.189   8273  Z= 0.328
  Chirality :  0.048   0.158   1012
  Planarity :  0.003   0.039   1010
  Dihedral  :  5.043  26.368    796
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 20.42 %
    Favored  : 74.52 %
  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 are not related in a simple way.
  whole: -1.63 (0.32), residues: 711
  helix: -0.36 (0.54), residues: 94
  sheet: -0.52 (0.33), residues: 279
  loop : -1.76 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.025   0.002   TYR A 104 
 PHE   0.015   0.002   PHE G 120 
 TRP   0.011   0.001   TRP C 137 
 HIS   0.005   0.001   HIS G 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 6141)
  covalent geometry    : angle       0.64564 ( 8273)
  hydrogen bonds       : bond        0.03658 (  150)
  hydrogen bonds       : angle       6.03131 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.4039 (mttt) cc_final: 0.2886 (tttt)
REVERT: B  137 TRP cc_start: 0.6294 (OUTLIER) cc_final: 0.5804 (m-90)
REVERT: C   99 MET cc_start: 0.5450 (ptp) cc_final: 0.5084 (ptp)
REVERT: D   89 ARG cc_start: 0.3694 (mmt180) cc_final: 0.3304 (mmt180)
REVERT: E   36 MET cc_start: 0.1300 (ptp) cc_final: 0.0057 (pmm)
REVERT: F   70 LEU cc_start: 0.7296 (mt) cc_final: 0.7044 (mt)
  outliers start: 34
  outliers final: 27
  residues processed: 126
  average time/residue: 0.0698
  time to fit residues: 12.3644
Evaluate side-chains
  132 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  113 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain G residue  180 THR
Chi-restraints excluded: chain G residue  186 HIS
Chi-restraints excluded: chain G residue  205 VAL
Chi-restraints excluded: chain G residue  257 ILE
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Chi-restraints excluded: chain G residue  290 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0970
   chunk 76 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0060
   overall best weight:    0.7598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.215253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.168991 restraints weight = 5337.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.171125 restraints weight = 6078.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.173505 restraints weight = 5046.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.175259 restraints weight = 3448.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.176253 restraints weight = 3141.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6046
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6141  Z= 0.143
  Angle     :  0.606  10.668   8273  Z= 0.305
  Chirality :  0.048   0.157   1012
  Planarity :  0.003   0.040   1010
  Dihedral  :  4.748  25.617    796
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 21.16 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.32), residues: 711
  helix: -0.20 (0.54), residues: 95
  sheet: -0.48 (0.33), residues: 279
  loop : -1.78 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.017   0.002   TYR A 104 
 PHE   0.013   0.001   PHE G 120 
 TRP   0.013   0.001   TRP C 137 
 HIS   0.004   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6141)
  covalent geometry    : angle       0.60609 ( 8273)
  hydrogen bonds       : bond        0.03296 (  150)
  hydrogen bonds       : angle       5.74398 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.214 
Fit side-chains
REVERT: B    1 MET cc_start: 0.6508 (tpt) cc_final: 0.5963 (tpt)
REVERT: B   24 LYS cc_start: 0.3922 (mttt) cc_final: 0.2796 (tttt)
REVERT: B   75 CYS cc_start: 0.6593 (m) cc_final: 0.6331 (t)
REVERT: B  137 TRP cc_start: 0.6130 (OUTLIER) cc_final: 0.5753 (m-90)
REVERT: C   99 MET cc_start: 0.5519 (ptp) cc_final: 0.5131 (ptp)
REVERT: D   89 ARG cc_start: 0.3720 (mmt180) cc_final: 0.3349 (mmt180)
REVERT: E   36 MET cc_start: 0.1326 (ptp) cc_final: 0.0107 (pmm)
REVERT: F   70 LEU cc_start: 0.7301 (mt) cc_final: 0.7035 (mt)
REVERT: G  289 MET cc_start: 0.7667 (ppp) cc_final: 0.7215 (ppp)
  outliers start: 31
  outliers final: 26
  residues processed: 126
  average time/residue: 0.0691
  time to fit residues: 12.1512
Evaluate side-chains
  133 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  113 VAL
Chi-restraints excluded: chain G residue  180 THR
Chi-restraints excluded: chain G residue  186 HIS
Chi-restraints excluded: chain G residue  205 VAL
Chi-restraints excluded: chain G residue  257 ILE
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Chi-restraints excluded: chain G residue  290 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 2 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0980
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.7960

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.214202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.168146 restraints weight = 5281.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.167376 restraints weight = 5272.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.169125 restraints weight = 5513.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.170351 restraints weight = 3893.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.171610 restraints weight = 3560.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6100
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6141  Z= 0.148
  Angle     :  0.628  11.321   8273  Z= 0.313
  Chirality :  0.048   0.152   1012
  Planarity :  0.003   0.041   1010
  Dihedral  :  4.798  25.330    796
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 22.06 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.32), residues: 711
  helix: -0.23 (0.54), residues: 95
  sheet: -0.51 (0.32), residues: 279
  loop : -1.75 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.019   0.002   TYR A 104 
 PHE   0.018   0.001   PHE G 150 
 TRP   0.013   0.001   TRP C 137 
 HIS   0.004   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6141)
  covalent geometry    : angle       0.62840 ( 8273)
  hydrogen bonds       : bond        0.03279 (  150)
  hydrogen bonds       : angle       5.71106 (  393)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.240 
Fit side-chains
REVERT: B   24 LYS cc_start: 0.3903 (mttt) cc_final: 0.3514 (ttmt)
REVERT: B  137 TRP cc_start: 0.6175 (OUTLIER) cc_final: 0.5841 (m-90)
REVERT: C   99 MET cc_start: 0.5555 (ptp) cc_final: 0.5155 (ptp)
REVERT: D   89 ARG cc_start: 0.3655 (mmt180) cc_final: 0.3288 (mmt180)
REVERT: E   36 MET cc_start: 0.1345 (ptp) cc_final: 0.0140 (pmm)
REVERT: F   70 LEU cc_start: 0.7375 (mt) cc_final: 0.7091 (mt)
REVERT: G  289 MET cc_start: 0.7726 (ppp) cc_final: 0.7236 (ppp)
  outliers start: 31
  outliers final: 28
  residues processed: 126
  average time/residue: 0.0714
  time to fit residues: 12.4595
Evaluate side-chains
  134 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  137 TRP
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain G residue  113 VAL
Chi-restraints excluded: chain G residue  180 THR
Chi-restraints excluded: chain G residue  186 HIS
Chi-restraints excluded: chain G residue  205 VAL
Chi-restraints excluded: chain G residue  257 ILE
Chi-restraints excluded: chain G residue  271 VAL
Chi-restraints excluded: chain G residue  281 SER
Chi-restraints excluded: chain G residue  283 VAL
Chi-restraints excluded: chain G residue  290 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 67 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.216605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.170334 restraints weight = 5230.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.169534 restraints weight = 5077.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.171614 restraints weight = 5204.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.173009 restraints weight = 3737.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.174182 restraints weight = 3508.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6105
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6141  Z= 0.130
  Angle     :  0.608  11.496   8273  Z= 0.301
  Chirality :  0.047   0.155   1012
  Planarity :  0.003   0.042   1010
  Dihedral  :  4.675  24.758    796
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 22.21 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.32), residues: 711
  helix: -0.09 (0.54), residues: 95
  sheet: -0.38 (0.33), residues: 272
  loop : -1.68 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  89 
 TYR   0.016   0.002   TYR A 104 
 PHE   0.014   0.001   PHE G 150 
 TRP   0.013   0.001   TRP C 137 
 HIS   0.003   0.001   HIS G 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6141)
  covalent geometry    : angle       0.60812 ( 8273)
  hydrogen bonds       : bond        0.03105 (  150)
  hydrogen bonds       : angle       5.56695 (  393)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1277.53 seconds
wall clock time: 22 minutes 52.02 seconds (1372.02 seconds total)