Starting phenix.real_space_refine
on Thu Jun 12 18:48:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn3_40611/06_2025/8sn3_40611.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn3_40611/06_2025/8sn3_40611.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/8sn3_40611/06_2025/8sn3_40611.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn3_40611/06_2025/8sn3_40611.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn3_40611/06_2025/8sn3_40611.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn3_40611/06_2025/8sn3_40611.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8276      2.51       5
     N    2716      2.21       5
     O    3291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14612
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 704
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 6, 'TRANS': 80}
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 601
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12313  SG  CYS K  31      31.696  74.358  48.206  1.00 55.65           S
  ATOM  12463  SG  CYS K  51      30.684  71.325  47.252  1.00 54.45           S
  ATOM  12487  SG  CYS K  54      31.262  73.831  44.365  1.00 65.71           S
  ATOM  12204  SG  CYS K  16      21.823  68.573  53.938  1.00 64.66           S
  ATOM  12222  SG  CYS K  19      19.688  65.906  55.446  1.00 64.84           S
  ATOM  12352  SG  CYS K  36      22.524  67.475  57.565  1.00 50.00           S
  ATOM  12374  SG  CYS K  39      23.418  65.177  54.865  1.00 54.15           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  76 " occ=0.25
  Time building chain proxies: 9.45, per 1000 atoms: 0.65
  Number of scatterers: 14612
  At special positions: 0
  Unit cell: (108.896, 134.128, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      33     16.00
     P     294     15.00
     O    3291      8.00
     N    2716      7.00
     C    8276      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 4.08
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 6


  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 11 sheets defined
      63.1% alpha, 4.5% beta
      135 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 6.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.659A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.773A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.748A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.523A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.713A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 122
      removed outlier: 3.714A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.513A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.649A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.505A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.002A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 74
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.534A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.527A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.673A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.837A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.774A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 4.669A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.861A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 90
      removed outlier: 3.792A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.710A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.549A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.564A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.900A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 41
    Processing helix  chain 'M' and resid 55 through 60
      removed outlier: 3.863A  pdb=" N   TYR M  59 " --> pdb=" O   THR M  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.873A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 8.120A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.878A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24
      removed outlier: 4.097A  pdb=" N   SER L  22 " --> pdb=" O   THR L  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15
      removed outlier: 3.627A  pdb=" N   ILE M  13 " --> pdb=" O   VAL M   5 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU M  69 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   HIS M  68 " --> pdb=" O   ILE M  44 " (cutoff:3.500A)

    493 hydrogen bonds defined for protein.
    1447 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      236 stacking parallelities
  Total time for adding SS restraints: 5.23

  Time building geometry restraints manager: 4.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3244
        1.33 -     1.45: 4467
        1.45 -     1.57: 7137
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15483
  Sorted by residual:
  bond pdb=" CD  LYS D 116 "
       pdb=" CE  LYS D 116 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.79e+00
  bond pdb=" CG  LYS D 116 "
       pdb=" CD  LYS D 116 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.63e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.454 -0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" CB  MET H  59 "
       pdb=" CG  MET H  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.11e+00
  bond pdb=" C3'  DA J -68 "
       pdb=" C2'  DA J -68 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.05e+00
  ... (remaining 15478 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 21491
        1.43 -     2.85: 626
        2.85 -     4.28: 39
        4.28 -     5.70: 22
        5.70 -     7.13: 4
  Bond angle restraints: 22182
  Sorted by residual:
  angle pdb=" N   VAL E 117 "
        pdb=" CA  VAL E 117 "
        pdb=" C   VAL E 117 "
      ideal   model   delta    sigma   weight residual
     111.90  108.81    3.09 8.10e-01 1.52e+00 1.45e+01
  angle pdb=" C   GLY G  37 "
        pdb=" N   ASN G  38 "
        pdb=" CA  ASN G  38 "
      ideal   model   delta    sigma   weight residual
     121.54  126.95   -5.41 1.91e+00 2.74e-01 8.03e+00
  angle pdb=" CA  LYS D 116 "
        pdb=" CB  LYS D 116 "
        pdb=" CG  LYS D 116 "
      ideal   model   delta    sigma   weight residual
     114.10  108.74    5.36 2.00e+00 2.50e-01 7.17e+00
  angle pdb=" C   ALA K  47 "
        pdb=" N   SER K  48 "
        pdb=" CA  SER K  48 "
      ideal   model   delta    sigma   weight residual
     122.55  117.60    4.95 2.03e+00 2.43e-01 5.94e+00
  angle pdb=" CB  MET H  59 "
        pdb=" CG  MET H  59 "
        pdb=" SD  MET H  59 "
      ideal   model   delta    sigma   weight residual
     112.70  105.57    7.13 3.00e+00 1.11e-01 5.65e+00
  ... (remaining 22177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 7303
       35.74 -    71.48: 1294
       71.48 -   107.22: 18
      107.22 -   142.96: 0
      142.96 -   178.70: 2
  Dihedral angle restraints: 8617
    sinusoidal: 5475
      harmonic: 3142
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.70 -178.70     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  GLN M  41 "
           pdb=" C   GLN M  41 "
           pdb=" N   ARG M  42 "
           pdb=" CA  ARG M  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.70   19.30     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.33  145.67     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 8614 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1731
       0.029 -    0.059: 577
       0.059 -    0.088: 134
       0.088 -    0.117: 66
       0.117 -    0.146: 8
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CA  ASN G  38 "
            pdb=" N   ASN G  38 "
            pdb=" C   ASN G  38 "
            pdb=" CB  ASN G  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE M  36 "
            pdb=" N   ILE M  36 "
            pdb=" C   ILE M  36 "
            pdb=" CB  ILE M  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1797
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  88 "   -0.019 2.00e-02 2.50e+03   1.74e-02 6.06e+00
        pdb=" CG  TYR F  88 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  88 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  88 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  88 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  88 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F  88 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO M  37 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO M  38 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO M  38 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO M  38 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  88 "    0.010 2.00e-02 2.50e+03   1.33e-02 3.53e+00
        pdb=" CG  TYR B  88 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  88 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  88 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  88 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  88 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  88 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  88 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1794 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 670
        2.71 -     3.26: 13349
        3.26 -     3.81: 26655
        3.81 -     4.35: 31370
        4.35 -     4.90: 46862
  Nonbonded interactions: 118906
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.164 2.496
  nonbonded pdb=" O   ARG L 139 "
            pdb=" NE2 GLN L 143 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR D  40 "
            pdb=" OP1  DG J  48 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NE2 GLN M  31 "
            pdb=" O   ILE M  36 "
     model   vdw
     2.291 3.120
  ... (remaining 118901 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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=0.25 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:             1.030
  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:             0.030
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     43.800
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
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      :  0.003   0.040  15492  Z= 0.159
  Angle     :  0.556   7.129  22194  Z= 0.322
  Chirality :  0.034   0.146   2516
  Planarity :  0.004   0.075   1795
  Dihedral  : 25.549 178.698   6581
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.26), residues: 1058
  helix:  2.28 (0.21), residues: 634
  sheet:  1.13 (0.76), residues: 46
  loop : -0.36 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L  33 
 HIS   0.002   0.000   HIS F  75 
 PHE   0.008   0.001   PHE K  53 
 TYR   0.043   0.002   TYR F  88 
 ARG   0.004   0.000   ARG M  74 

Details of bonding type rmsd
  link_TRANS           : bond        0.00037 (    2)
  link_TRANS           : angle       0.15453 (    6)
  hydrogen bonds       : bond        0.11169 (  840)
  hydrogen bonds       : angle       4.09895 ( 2137)
  metal coordination   : bond        0.00134 (    7)
  metal coordination   : angle       3.36711 (    6)
  covalent geometry    : bond        0.00348 (15483)
  covalent geometry    : angle       0.55324 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8701 (tttm)
REVERT: D   68 ASP cc_start: 0.8310 (t70) cc_final: 0.7858 (t0)
REVERT: G   36 LYS cc_start: 0.8763 (mptt) cc_final: 0.8418 (mmtm)
REVERT: H  120 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9041 (ttmt)
REVERT: K   41 GLN cc_start: 0.8920 (tp40) cc_final: 0.8709 (tp40)
REVERT: K   68 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6713 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.3449
  time to fit residues: 103.4982
Evaluate side-chains
  182 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0980
   chunk 65 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  79 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.147043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.104947 restraints weight = 30168.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.107502 restraints weight = 49772.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.107725 restraints weight = 33750.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3129
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15492  Z= 0.163
  Angle     :  0.574  10.146  22194  Z= 0.328
  Chirality :  0.034   0.170   2516
  Planarity :  0.004   0.036   1795
  Dihedral  : 28.771 178.849   4412
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.92 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.26), residues: 1058
  helix:  2.34 (0.21), residues: 651
  sheet:  1.32 (0.87), residues: 38
  loop : -0.53 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP L 141 
 HIS   0.004   0.001   HIS L  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.033   0.002   TYR H  83 
 ARG   0.011   0.000   ARG L  72 

Details of bonding type rmsd
  link_TRANS           : bond        0.00036 (    2)
  link_TRANS           : angle       0.18617 (    6)
  hydrogen bonds       : bond        0.04854 (  840)
  hydrogen bonds       : angle       3.45077 ( 2137)
  metal coordination   : bond        0.00202 (    7)
  metal coordination   : angle       3.26070 (    6)
  covalent geometry    : bond        0.00356 (15483)
  covalent geometry    : angle       0.57183 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8691 (tttm)
REVERT: D   40 TYR cc_start: 0.9373 (m-80) cc_final: 0.9085 (m-80)
REVERT: D   59 MET cc_start: 0.8707 (tpp) cc_final: 0.8496 (tpp)
REVERT: D   68 ASP cc_start: 0.8300 (t70) cc_final: 0.7949 (t0)
REVERT: D   83 TYR cc_start: 0.7835 (m-10) cc_final: 0.7179 (m-80)
REVERT: G   36 LYS cc_start: 0.8909 (mptt) cc_final: 0.8632 (mmtm)
REVERT: H   42 TYR cc_start: 0.8574 (t80) cc_final: 0.8168 (t80)
REVERT: H  120 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8947 (ttpt)
REVERT: L    5 ARG cc_start: 0.8365 (tpt90) cc_final: 0.7763 (tpt90)
REVERT: L    9 GLU cc_start: 0.7135 (tt0) cc_final: 0.6573 (tt0)
REVERT: L  147 MET cc_start: 0.4468 (mpp) cc_final: 0.4009 (mpp)
REVERT: M    1 MET cc_start: -0.0912 (OUTLIER) cc_final: -0.1122 (ptt)
  outliers start: 18
  outliers final: 12
  residues processed: 199
  average time/residue: 0.4303
  time to fit residues: 117.7814
Evaluate side-chains
  189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain M residue    1 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 106 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
D  95 GLN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.146931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.105539 restraints weight = 35212.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.110928 restraints weight = 59490.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110687 restraints weight = 22307.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15492  Z= 0.159
  Angle     :  0.565  11.241  22194  Z= 0.321
  Chirality :  0.034   0.132   2516
  Planarity :  0.004   0.036   1795
  Dihedral  : 28.840 179.052   4412
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.19 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.26), residues: 1058
  helix:  2.41 (0.21), residues: 650
  sheet:  0.75 (0.88), residues: 36
  loop : -0.60 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP L  33 
 HIS   0.002   0.001   HIS H  82 
 PHE   0.013   0.001   PHE L  62 
 TYR   0.010   0.001   TYR D  40 
 ARG   0.007   0.000   ARG H  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00003 (    2)
  link_TRANS           : angle       0.26216 (    6)
  hydrogen bonds       : bond        0.04692 (  840)
  hydrogen bonds       : angle       3.39172 ( 2137)
  metal coordination   : bond        0.00238 (    7)
  metal coordination   : angle       3.94666 (    6)
  covalent geometry    : bond        0.00351 (15483)
  covalent geometry    : angle       0.56119 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 1.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8447 (pp30) cc_final: 0.8215 (pp30)
REVERT: B   88 TYR cc_start: 0.8662 (m-10) cc_final: 0.7992 (m-10)
REVERT: C   95 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8705 (tttm)
REVERT: D   40 TYR cc_start: 0.9391 (m-80) cc_final: 0.9148 (m-80)
REVERT: D   59 MET cc_start: 0.8844 (tpp) cc_final: 0.8581 (tpp)
REVERT: D   68 ASP cc_start: 0.8344 (t70) cc_final: 0.7987 (t0)
REVERT: D   83 TYR cc_start: 0.7749 (m-10) cc_final: 0.7535 (m-10)
REVERT: G   36 LYS cc_start: 0.8936 (mptt) cc_final: 0.8632 (mmtm)
REVERT: H   42 TYR cc_start: 0.8611 (t80) cc_final: 0.8156 (t80)
REVERT: H  120 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8913 (ttpt)
REVERT: L    5 ARG cc_start: 0.8324 (tpt90) cc_final: 0.7816 (tpt-90)
REVERT: L    9 GLU cc_start: 0.7238 (tt0) cc_final: 0.6639 (tt0)
REVERT: L   63 LYS cc_start: 0.8922 (mppt) cc_final: 0.8713 (mptt)
REVERT: L  101 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8546 (mmmm)
REVERT: L  109 LEU cc_start: 0.8797 (tt) cc_final: 0.8564 (tt)
REVERT: L  147 MET cc_start: 0.4598 (mpp) cc_final: 0.4057 (mpp)
  outliers start: 22
  outliers final: 17
  residues processed: 199
  average time/residue: 0.3767
  time to fit residues: 104.7833
Evaluate side-chains
  191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain K residue   27 VAL
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   51 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 112 optimal weight:    0.0870
   chunk 102 optimal weight:    0.0980
   chunk 10 optimal weight:    0.5980
   chunk 78 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0040
   chunk 58 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.2970

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
D  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.148608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.107243 restraints weight = 31285.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.109555 restraints weight = 52269.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.110262 restraints weight = 32197.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15492  Z= 0.136
  Angle     :  0.551  11.984  22194  Z= 0.312
  Chirality :  0.033   0.210   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 28.797 179.361   4412
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.59 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.26), residues: 1058
  helix:  2.48 (0.21), residues: 649
  sheet:  0.60 (0.85), residues: 36
  loop : -0.52 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L  33 
 HIS   0.002   0.000   HIS B  75 
 PHE   0.018   0.001   PHE L  62 
 TYR   0.014   0.001   TYR F  88 
 ARG   0.007   0.000   ARG H  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00086 (    2)
  link_TRANS           : angle       0.06225 (    6)
  hydrogen bonds       : bond        0.04176 (  840)
  hydrogen bonds       : angle       3.25964 ( 2137)
  metal coordination   : bond        0.00262 (    7)
  metal coordination   : angle       3.66930 (    6)
  covalent geometry    : bond        0.00285 (15483)
  covalent geometry    : angle       0.54785 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 194
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8359 (pp30) cc_final: 0.8144 (pp30)
REVERT: B   88 TYR cc_start: 0.8544 (m-10) cc_final: 0.7842 (m-10)
REVERT: C   95 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8689 (tttm)
REVERT: D   40 TYR cc_start: 0.9359 (m-80) cc_final: 0.9077 (m-80)
REVERT: D   59 MET cc_start: 0.8728 (tpp) cc_final: 0.8361 (tpp)
REVERT: D   68 ASP cc_start: 0.8109 (t70) cc_final: 0.7752 (t0)
REVERT: D   71 GLU cc_start: 0.7897 (tp30) cc_final: 0.7442 (tp30)
REVERT: D   83 TYR cc_start: 0.7667 (m-10) cc_final: 0.7427 (m-10)
REVERT: E  125 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7244 (mt0)
REVERT: G   36 LYS cc_start: 0.8897 (mptt) cc_final: 0.8559 (mmtm)
REVERT: H   42 TYR cc_start: 0.8548 (t80) cc_final: 0.8110 (t80)
REVERT: H  120 LYS cc_start: 0.9195 (ttpt) cc_final: 0.8915 (ttpt)
REVERT: L    5 ARG cc_start: 0.8173 (tpt90) cc_final: 0.7855 (tpt-90)
REVERT: L    9 GLU cc_start: 0.7001 (tt0) cc_final: 0.6533 (tt0)
REVERT: L   56 PHE cc_start: 0.8046 (m-80) cc_final: 0.7746 (m-10)
REVERT: L   63 LYS cc_start: 0.8884 (mppt) cc_final: 0.8662 (mptt)
REVERT: L   69 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6204 (m-10)
REVERT: L  101 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8479 (mmmm)
REVERT: L  109 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8525 (tt)
REVERT: L  147 MET cc_start: 0.4414 (mpp) cc_final: 0.3821 (mpp)
  outliers start: 19
  outliers final: 9
  residues processed: 204
  average time/residue: 0.3708
  time to fit residues: 103.3484
Evaluate side-chains
  190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 44 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 105 optimal weight:    0.6980
   chunk 127 optimal weight:    0.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.147405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.105992 restraints weight = 37121.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.110458 restraints weight = 58449.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.110857 restraints weight = 24688.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15492  Z= 0.151
  Angle     :  0.558  12.639  22194  Z= 0.316
  Chirality :  0.034   0.162   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 28.890 179.071   4412
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.00 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.26), residues: 1058
  helix:  2.43 (0.21), residues: 651
  sheet:  0.64 (0.84), residues: 36
  loop : -0.56 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP K  77 
 HIS   0.003   0.000   HIS K  65 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.007   0.000   ARG H  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00030 (    2)
  link_TRANS           : angle       0.07189 (    6)
  hydrogen bonds       : bond        0.04467 (  840)
  hydrogen bonds       : angle       3.34783 ( 2137)
  metal coordination   : bond        0.00316 (    7)
  metal coordination   : angle       3.92675 (    6)
  covalent geometry    : bond        0.00333 (15483)
  covalent geometry    : angle       0.55393 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 2.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8686 (m-10) cc_final: 0.7978 (m-10)
REVERT: C   95 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8701 (tttm)
REVERT: D   68 ASP cc_start: 0.8192 (t70) cc_final: 0.7691 (t0)
REVERT: D   83 TYR cc_start: 0.7849 (m-10) cc_final: 0.7646 (m-10)
REVERT: E  125 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7214 (mt0)
REVERT: G   36 LYS cc_start: 0.8925 (mptt) cc_final: 0.8499 (mttm)
REVERT: H   42 TYR cc_start: 0.8594 (t80) cc_final: 0.8147 (t80)
REVERT: H  120 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8906 (ttpt)
REVERT: K   77 TRP cc_start: 0.7605 (t-100) cc_final: 0.7064 (t-100)
REVERT: L    5 ARG cc_start: 0.8267 (tpt90) cc_final: 0.8013 (tpt-90)
REVERT: L    9 GLU cc_start: 0.7432 (tt0) cc_final: 0.6857 (tt0)
REVERT: L   63 LYS cc_start: 0.8950 (mppt) cc_final: 0.8732 (mptt)
REVERT: L   69 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6224 (m-10)
REVERT: L  101 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8594 (mmmm)
REVERT: L  109 LEU cc_start: 0.8840 (tt) cc_final: 0.8599 (tt)
REVERT: L  147 MET cc_start: 0.4546 (mpp) cc_final: 0.3876 (mpp)
  outliers start: 20
  outliers final: 13
  residues processed: 195
  average time/residue: 0.5053
  time to fit residues: 136.4824
Evaluate side-chains
  191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   chunk 128 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
G  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.147191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.103626 restraints weight = 26741.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.101606 restraints weight = 33440.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102694 restraints weight = 29997.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15492  Z= 0.156
  Angle     :  0.576  13.439  22194  Z= 0.323
  Chirality :  0.034   0.224   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 28.908 179.298   4412
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.76 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.27), residues: 1058
  helix:  2.43 (0.21), residues: 651
  sheet:  0.69 (0.85), residues: 36
  loop : -0.56 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  33 
 HIS   0.002   0.000   HIS F  75 
 PHE   0.013   0.001   PHE L  56 
 TYR   0.013   0.001   TYR H  83 
 ARG   0.007   0.000   ARG H  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00030 (    2)
  link_TRANS           : angle       0.05772 (    6)
  hydrogen bonds       : bond        0.04536 (  840)
  hydrogen bonds       : angle       3.37751 ( 2137)
  metal coordination   : bond        0.00299 (    7)
  metal coordination   : angle       4.22599 (    6)
  covalent geometry    : bond        0.00346 (15483)
  covalent geometry    : angle       0.57207 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8811 (m-10) cc_final: 0.8243 (m-10)
REVERT: C   95 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8802 (tttm)
REVERT: D   42 TYR cc_start: 0.8567 (t80) cc_final: 0.8314 (t80)
REVERT: D   59 MET cc_start: 0.8828 (tpp) cc_final: 0.8585 (tpp)
REVERT: D   68 ASP cc_start: 0.8191 (t70) cc_final: 0.7687 (t0)
REVERT: E  125 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7142 (mt0)
REVERT: G   36 LYS cc_start: 0.8988 (mptt) cc_final: 0.8590 (mttm)
REVERT: H   33 ARG cc_start: 0.6834 (mtm180) cc_final: 0.6441 (mtm180)
REVERT: H   42 TYR cc_start: 0.8590 (t80) cc_final: 0.8120 (t80)
REVERT: H  120 LYS cc_start: 0.9232 (ttpt) cc_final: 0.8905 (ttpt)
REVERT: K   20 MET cc_start: 0.7381 (mmm) cc_final: 0.6428 (mmt)
REVERT: K   77 TRP cc_start: 0.7697 (t-100) cc_final: 0.7181 (t-100)
REVERT: L    5 ARG cc_start: 0.8300 (tpt90) cc_final: 0.7754 (tpt-90)
REVERT: L    9 GLU cc_start: 0.7414 (tt0) cc_final: 0.6396 (tt0)
REVERT: L   56 PHE cc_start: 0.8011 (m-80) cc_final: 0.7752 (m-10)
REVERT: L   63 LYS cc_start: 0.8995 (mppt) cc_final: 0.8791 (mptt)
REVERT: L   69 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6183 (m-10)
REVERT: L  101 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8560 (mmmm)
REVERT: L  109 LEU cc_start: 0.8819 (tt) cc_final: 0.8567 (tt)
REVERT: L  147 MET cc_start: 0.4534 (mpp) cc_final: 0.3837 (mpp)
  outliers start: 25
  outliers final: 18
  residues processed: 197
  average time/residue: 0.3578
  time to fit residues: 96.7369
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 124 optimal weight:   30.0000
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
G  73 ASN
M  31 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.147284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 116)---------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.091479 restraints weight = 42540.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.092908 restraints weight = 28568.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.092752 restraints weight = 21147.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15492  Z= 0.151
  Angle     :  0.568  12.832  22194  Z= 0.319
  Chirality :  0.034   0.197   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 28.903 179.461   4412
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.30 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.26), residues: 1058
  helix:  2.41 (0.21), residues: 650
  sheet:  0.68 (0.86), residues: 36
  loop : -0.57 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L  33 
 HIS   0.003   0.000   HIS F  75 
 PHE   0.008   0.001   PHE L  56 
 TYR   0.014   0.001   TYR H  83 
 ARG   0.007   0.000   ARG H  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00046 (    2)
  link_TRANS           : angle       0.03423 (    6)
  hydrogen bonds       : bond        0.04484 (  840)
  hydrogen bonds       : angle       3.33443 ( 2137)
  metal coordination   : bond        0.00307 (    7)
  metal coordination   : angle       4.23385 (    6)
  covalent geometry    : bond        0.00333 (15483)
  covalent geometry    : angle       0.56345 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 184
  time to evaluate  : 2.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8610 (m-10) cc_final: 0.8186 (m-10)
REVERT: C   95 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8817 (tttm)
REVERT: D   42 TYR cc_start: 0.8565 (t80) cc_final: 0.8248 (t80)
REVERT: D   68 ASP cc_start: 0.8215 (t70) cc_final: 0.7878 (t0)
REVERT: D   71 GLU cc_start: 0.7996 (tp30) cc_final: 0.7585 (tp30)
REVERT: E  125 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7338 (mt0)
REVERT: G   36 LYS cc_start: 0.9011 (mptt) cc_final: 0.8612 (mttm)
REVERT: H   33 ARG cc_start: 0.6906 (mtm180) cc_final: 0.6508 (mtm180)
REVERT: H   42 TYR cc_start: 0.8552 (t80) cc_final: 0.8071 (t80)
REVERT: H  120 LYS cc_start: 0.9229 (ttpt) cc_final: 0.8816 (ttpt)
REVERT: K   20 MET cc_start: 0.7042 (mmm) cc_final: 0.6645 (mmt)
REVERT: K   77 TRP cc_start: 0.8099 (t-100) cc_final: 0.7602 (t-100)
REVERT: L    5 ARG cc_start: 0.9309 (tpt90) cc_final: 0.8883 (tpt-90)
REVERT: L    7 ASN cc_start: 0.9346 (m-40) cc_final: 0.8777 (p0)
REVERT: L    9 GLU cc_start: 0.8554 (tt0) cc_final: 0.8097 (tt0)
REVERT: L   56 PHE cc_start: 0.8423 (m-80) cc_final: 0.8010 (m-10)
REVERT: L   63 LYS cc_start: 0.8854 (mppt) cc_final: 0.8629 (mptt)
REVERT: L   69 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.6845 (m-10)
REVERT: L  101 LYS cc_start: 0.9408 (mmtm) cc_final: 0.9101 (mmmm)
REVERT: L  109 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8999 (tt)
REVERT: L  147 MET cc_start: 0.6217 (mpp) cc_final: 0.5388 (mpp)
  outliers start: 24
  outliers final: 16
  residues processed: 196
  average time/residue: 0.4675
  time to fit residues: 127.8289
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 85 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.146552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.104093 restraints weight = 32745.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.106935 restraints weight = 55225.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107672 restraints weight = 30631.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15492  Z= 0.169
  Angle     :  0.598  14.076  22194  Z= 0.329
  Chirality :  0.035   0.324   2516
  Planarity :  0.004   0.040   1795
  Dihedral  : 28.948 179.403   4412
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.41 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.27), residues: 1058
  helix:  2.35 (0.21), residues: 649
  sheet:  0.92 (0.86), residues: 36
  loop : -0.56 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L  33 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.025   0.001   PHE L  62 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.015   0.000   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00039 (    2)
  link_TRANS           : angle       0.08703 (    6)
  hydrogen bonds       : bond        0.04756 (  840)
  hydrogen bonds       : angle       3.42625 ( 2137)
  metal coordination   : bond        0.00302 (    7)
  metal coordination   : angle       4.40856 (    6)
  covalent geometry    : bond        0.00382 (15483)
  covalent geometry    : angle       0.59417 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8542 (m-10) cc_final: 0.8121 (m-10)
REVERT: C   95 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8708 (tttm)
REVERT: D   42 TYR cc_start: 0.8627 (t80) cc_final: 0.8339 (t80)
REVERT: D   68 ASP cc_start: 0.8210 (t70) cc_final: 0.7718 (t0)
REVERT: E  125 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7252 (mt0)
REVERT: F   72 TYR cc_start: 0.8616 (m-80) cc_final: 0.8338 (m-80)
REVERT: G   36 LYS cc_start: 0.8952 (mptt) cc_final: 0.8528 (mttm)
REVERT: H   33 ARG cc_start: 0.6847 (mtm180) cc_final: 0.6486 (mtm180)
REVERT: H   42 TYR cc_start: 0.8618 (t80) cc_final: 0.8152 (t80)
REVERT: H  120 LYS cc_start: 0.9232 (ttpt) cc_final: 0.8906 (ttpt)
REVERT: K   20 MET cc_start: 0.7458 (mmm) cc_final: 0.6472 (mmt)
REVERT: K   46 LYS cc_start: 0.7962 (ptpt) cc_final: 0.7684 (ptpt)
REVERT: L    9 GLU cc_start: 0.6673 (tt0) cc_final: 0.6459 (tt0)
REVERT: L   56 PHE cc_start: 0.8253 (m-80) cc_final: 0.8027 (m-10)
REVERT: L   69 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6188 (m-10)
REVERT: L  101 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8546 (mmmm)
REVERT: L  109 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8539 (tt)
REVERT: L  147 MET cc_start: 0.4410 (mpp) cc_final: 0.3622 (mpp)
  outliers start: 26
  outliers final: 21
  residues processed: 192
  average time/residue: 0.3199
  time to fit residues: 84.1315
Evaluate side-chains
  198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0970
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.146004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.107666 restraints weight = 37481.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.110624 restraints weight = 73577.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.111548 restraints weight = 32448.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15492  Z= 0.176
  Angle     :  0.612  14.490  22194  Z= 0.337
  Chirality :  0.036   0.338   2516
  Planarity :  0.004   0.033   1795
  Dihedral  : 28.981 179.597   4412
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.95 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.26), residues: 1058
  helix:  2.25 (0.21), residues: 651
  sheet:  1.04 (0.82), residues: 41
  loop : -0.61 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP L  33 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.031   0.001   PHE L  62 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.014   0.000   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00036 (    2)
  link_TRANS           : angle       0.10152 (    6)
  hydrogen bonds       : bond        0.04901 (  840)
  hydrogen bonds       : angle       3.51373 ( 2137)
  metal coordination   : bond        0.00363 (    7)
  metal coordination   : angle       4.60825 (    6)
  covalent geometry    : bond        0.00401 (15483)
  covalent geometry    : angle       0.60723 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8662 (tttm)
REVERT: D   42 TYR cc_start: 0.8583 (t80) cc_final: 0.8306 (t80)
REVERT: D   68 ASP cc_start: 0.8278 (t70) cc_final: 0.7792 (t0)
REVERT: E  125 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7218 (mt0)
REVERT: F   59 LYS cc_start: 0.8269 (tttt) cc_final: 0.8017 (ttpm)
REVERT: G   36 LYS cc_start: 0.8847 (mptt) cc_final: 0.8450 (mttm)
REVERT: H   33 ARG cc_start: 0.6842 (mtm180) cc_final: 0.6475 (mtm180)
REVERT: H   42 TYR cc_start: 0.8617 (t80) cc_final: 0.8159 (t80)
REVERT: H  120 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8923 (ttpt)
REVERT: K   46 LYS cc_start: 0.8065 (ptpt) cc_final: 0.7735 (ptpt)
REVERT: L   69 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6064 (m-10)
REVERT: L  101 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8377 (mmmm)
REVERT: L  147 MET cc_start: 0.4055 (mpp) cc_final: 0.3474 (mpp)
  outliers start: 25
  outliers final: 20
  residues processed: 192
  average time/residue: 0.3332
  time to fit residues: 87.7561
Evaluate side-chains
  194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 126 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 85 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 119 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.146890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105862 restraints weight = 28983.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.103780 restraints weight = 45985.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.105299 restraints weight = 43299.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15492  Z= 0.154
  Angle     :  0.608  14.386  22194  Z= 0.335
  Chirality :  0.035   0.335   2516
  Planarity :  0.004   0.045   1795
  Dihedral  : 28.943 179.983   4412
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.59 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.26), residues: 1058
  helix:  2.29 (0.21), residues: 652
  sheet:  1.11 (0.84), residues: 41
  loop : -0.56 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.004   TRP K  77 
 HIS   0.003   0.000   HIS F  75 
 PHE   0.010   0.001   PHE L  62 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.015   0.000   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00062 (    2)
  link_TRANS           : angle       0.05361 (    6)
  hydrogen bonds       : bond        0.04628 (  840)
  hydrogen bonds       : angle       3.40052 ( 2137)
  metal coordination   : bond        0.00318 (    7)
  metal coordination   : angle       4.79805 (    6)
  covalent geometry    : bond        0.00342 (15483)
  covalent geometry    : angle       0.60348 (22182)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 177
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9112 (mttm) cc_final: 0.8546 (mttm)
REVERT: C   95 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8687 (tttm)
REVERT: D   42 TYR cc_start: 0.8652 (t80) cc_final: 0.8339 (t80)
REVERT: D   68 ASP cc_start: 0.8142 (t70) cc_final: 0.7663 (t0)
REVERT: D   71 GLU cc_start: 0.7771 (tp30) cc_final: 0.7478 (tp30)
REVERT: E   90 MET cc_start: 0.8514 (mmm) cc_final: 0.8313 (mmm)
REVERT: E  125 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7279 (mt0)
REVERT: G   36 LYS cc_start: 0.8948 (mptt) cc_final: 0.8547 (mttm)
REVERT: H   33 ARG cc_start: 0.6857 (mtm180) cc_final: 0.6485 (mtm180)
REVERT: H   42 TYR cc_start: 0.8568 (t80) cc_final: 0.8076 (t80)
REVERT: H  120 LYS cc_start: 0.9238 (ttpt) cc_final: 0.8904 (ttpt)
REVERT: K   20 MET cc_start: 0.7420 (mmm) cc_final: 0.6841 (mmm)
REVERT: K   41 GLN cc_start: 0.8460 (tp40) cc_final: 0.8051 (tp40)
REVERT: K   46 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7967 (ptpt)
REVERT: K   68 ARG cc_start: 0.7606 (mmp80) cc_final: 0.6609 (ptm-80)
REVERT: L    7 ASN cc_start: 0.8624 (m-40) cc_final: 0.8074 (p0)
REVERT: L   69 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6143 (m-10)
REVERT: L  101 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8507 (mmmm)
REVERT: L  147 MET cc_start: 0.4203 (mpp) cc_final: 0.3631 (mpp)
  outliers start: 20
  outliers final: 16
  residues processed: 187
  average time/residue: 0.3445
  time to fit residues: 88.4627
Evaluate side-chains
  193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 113 optimal weight:    7.9990
   chunk 95 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0670
   chunk 99 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0870
   chunk 62 optimal weight:    0.0020
   chunk 102 optimal weight:    0.7980
   chunk 105 optimal weight:    0.7980
   chunk 78 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   overall best weight:    0.3304

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
G  73 ASN
K  73 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.149259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.104895 restraints weight = 26315.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.103153 restraints weight = 29231.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.104162 restraints weight = 28696.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15492  Z= 0.140
  Angle     :  0.603  15.419  22194  Z= 0.331
  Chirality :  0.036   0.465   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 28.834 179.976   4412
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.24 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.27), residues: 1058
  helix:  2.32 (0.21), residues: 655
  sheet:  0.90 (0.85), residues: 42
  loop : -0.55 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP K  77 
 HIS   0.002   0.000   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.019   0.001   TYR L  60 
 ARG   0.008   0.000   ARG H  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00118 (    2)
  link_TRANS           : angle       0.12139 (    6)
  hydrogen bonds       : bond        0.04179 (  840)
  hydrogen bonds       : angle       3.31820 ( 2137)
  metal coordination   : bond        0.00302 (    7)
  metal coordination   : angle       4.21213 (    6)
  covalent geometry    : bond        0.00299 (15483)
  covalent geometry    : angle       0.59944 (22182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5423.81 seconds
wall clock time: 98 minutes 50.68 seconds (5930.68 seconds total)