Starting phenix.real_space_refine
on Mon Jul 28 23:53:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mxl_24073/07_2025/7mxl_24073.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mxl_24073/07_2025/7mxl_24073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mxl_24073/07_2025/7mxl_24073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mxl_24073/07_2025/7mxl_24073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mxl_24073/07_2025/7mxl_24073.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mxl_24073/07_2025/7mxl_24073.cif"
  }
  resolution = 3.2
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    6850      2.51       5
     N    1817      2.21       5
     O    2162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10866
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1553
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 193}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1554
          Classifications: {'peptide': 200}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 186}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1233
          Classifications: {'peptide': 159}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 150}
    Chain: "J"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1618
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201}
          Chain breaks: 2
    Chain: "K"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1650
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1632
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
    Chain: "H"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1626
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206}
  Time building chain proxies: 6.87, per 1000 atoms: 0.63
  Number of scatterers: 10866
  At special positions: 0
  Unit cell: (114.4, 148.72, 144.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    2162      8.00
     N    1817      7.00
     C    6850      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 134 " - pdb=" SG  CYS K 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 147 " - pdb=" SG  CYS J 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 135 " - pdb=" SG  CYS K 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 202 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2634

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 34 sheets defined
      9.6% alpha, 47.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 66
      No H-bonds generated for 'chain 'A' and resid 64 through 66'
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.677A  pdb=" N   THR A  91 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.573A  pdb=" N   ASP B  82 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   PHE B  83 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 79 through 83'
    Processing helix  chain 'B' and resid 121 through 128
    Processing helix  chain 'C' and resid 15 through 24
    Processing helix  chain 'C' and resid 25 through 28
      removed outlier: 4.588A  pdb=" N   ASP C  28 " --> pdb=" O   LEU C  25 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 25 through 28'
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'C' and resid 130 through 155
    Processing helix  chain 'J' and resid 28 through 32
      removed outlier: 3.624A  pdb=" N   TYR J  32 " --> pdb=" O   PHE J  29 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 87 through 91
      removed outlier: 4.028A  pdb=" N   THR J  91 " --> pdb=" O   SER J  88 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 29 through 32
    Processing helix  chain 'K' and resid 80 through 84
      removed outlier: 3.980A  pdb=" N   PHE K  84 " --> pdb=" O   PRO K  81 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 122 through 129
    Processing helix  chain 'K' and resid 184 through 188
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.547A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing helix  chain 'L' and resid 121 through 128
      removed outlier: 3.532A  pdb=" N   LEU L 125 " --> pdb=" O   SER L 121 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS L 126 " --> pdb=" O   ASP L 122 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 188
      removed outlier: 3.512A  pdb=" N   LYS L 188 " --> pdb=" O   ALA L 184 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.862A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.793A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 162 through 164
      No H-bonds generated for 'chain 'H' and resid 162 through 164'
    Processing helix  chain 'H' and resid 191 through 195
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.592A  pdb=" N   TRP A  37 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR A  51 " --> pdb=" O   TRP A  35 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP A  35 " --> pdb=" O   TYR A  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.592A  pdb=" N   TRP A  37 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR A  51 " --> pdb=" O   TRP A  35 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP A  35 " --> pdb=" O   TYR A  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127
      removed outlier: 6.036A  pdb=" N   TYR A 180 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 127
      removed outlier: 6.036A  pdb=" N   TYR A 180 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 158
      removed outlier: 3.542A  pdb=" N   THR A 155 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13
      removed outlier: 7.009A  pdb=" N   LEU B  11 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118
    Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 196
    Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 12
      removed outlier: 3.875A  pdb=" N   LYS C  98 " --> pdb=" O   HIS C 122 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   GLU C  97 " --> pdb=" O   GLU C  88 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   GLU C  88 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LYS C  69 " --> pdb=" O   ILE C  87 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   GLY C  89 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   TYR C  67 " --> pdb=" O   GLY C  89 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE C  54 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 12
      removed outlier: 3.875A  pdb=" N   LYS C  98 " --> pdb=" O   HIS C 122 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   GLU C  97 " --> pdb=" O   GLU C  88 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   GLU C  88 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 3 through 6
    Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.470A  pdb=" N   ILE J  34 " --> pdb=" O   TRP J  50 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP J  50 " --> pdb=" O   ILE J  34 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   TRP J  36 " --> pdb=" O   MET J  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'J' and resid 10 through 12
      removed outlier: 4.276A  pdb=" N   TYR J 109 " --> pdb=" O   ARG J  98 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'J' and resid 127 through 131
      removed outlier: 6.198A  pdb=" N   TYR J 183 " --> pdb=" O   ASP J 151 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'J' and resid 127 through 131
      removed outlier: 6.198A  pdb=" N   TYR J 183 " --> pdb=" O   ASP J 151 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'J' and resid 158 through 161
    Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 7
    Processing sheet with id=AC2, first strand: chain 'K' and resid 12 through 13
      removed outlier: 3.773A  pdb=" N   LEU K  13 " --> pdb=" O   GLU K 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'K' and resid 54 through 55
      removed outlier: 6.428A  pdb=" N   TRP K  36 " --> pdb=" O   LEU K  48 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   TYR K  50 " --> pdb=" O   LEU K  34 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU K  34 " --> pdb=" O   TYR K  50 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'K' and resid 118 through 119
      removed outlier: 3.676A  pdb=" N   VAL K 134 " --> pdb=" O   PHE K 119 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   TYR K 174 " --> pdb=" O   ASN K 139 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'K' and resid 145 through 151
      removed outlier: 4.020A  pdb=" N   LYS K 146 " --> pdb=" O   THR K 198 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   TYR K 193 " --> pdb=" O   PHE K 210 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.231A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.231A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'L' and resid 19 through 24
    Processing sheet with id=AC9, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.573A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.630A  pdb=" N   LYS L 207 " --> pdb=" O   CYS L 194 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.844A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.724A  pdb=" N   ASN H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'H' and resid 126 through 130
      removed outlier: 5.883A  pdb=" N   TYR H 182 " --> pdb=" O   ASP H 150 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'H' and resid 126 through 130
      removed outlier: 5.883A  pdb=" N   TYR H 182 " --> pdb=" O   ASP H 150 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'H' and resid 157 through 160

    512 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.76

  Time building geometry restraints manager: 3.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3469
        1.34 -     1.46: 2735
        1.46 -     1.58: 4872
        1.58 -     1.70: 0
        1.70 -     1.82: 45
  Bond restraints: 11121
  Sorted by residual:
  bond pdb=" CG1 ILE H 101 "
       pdb=" CD1 ILE H 101 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.79e-01
  bond pdb=" CA  ASN A 208 "
       pdb=" CB  ASN A 208 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 9.65e-01
  bond pdb=" CG1 ILE C  92 "
       pdb=" CD1 ILE C  92 "
    ideal  model  delta    sigma   weight residual
    1.513  1.476  0.037 3.90e-02 6.57e+02 8.86e-01
  bond pdb=" CB  ASN A 208 "
       pdb=" CG  ASN A 208 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.42e-01
  bond pdb=" CB  LYS A 205 "
       pdb=" CG  LYS A 205 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.96e-01
  ... (remaining 11116 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 14654
        1.52 -     3.05: 402
        3.05 -     4.57: 52
        4.57 -     6.10: 12
        6.10 -     7.62: 4
  Bond angle restraints: 15124
  Sorted by residual:
  angle pdb=" C   GLU J 155 "
        pdb=" N   PRO J 156 "
        pdb=" CD  PRO J 156 "
      ideal   model   delta    sigma   weight residual
     120.60  114.33    6.27 2.20e+00 2.07e-01 8.13e+00
  angle pdb=" N   ILE J  30 "
        pdb=" CA  ILE J  30 "
        pdb=" C   ILE J  30 "
      ideal   model   delta    sigma   weight residual
     113.00  109.36    3.64 1.30e+00 5.92e-01 7.85e+00
  angle pdb=" N   LYS A 121 "
        pdb=" CA  LYS A 121 "
        pdb=" C   LYS A 121 "
      ideal   model   delta    sigma   weight residual
     108.34  111.90   -3.56 1.31e+00 5.83e-01 7.39e+00
  angle pdb=" C   SER A 207 "
        pdb=" N   ASN A 208 "
        pdb=" CA  ASN A 208 "
      ideal   model   delta    sigma   weight residual
     121.54  126.44   -4.90 1.91e+00 2.74e-01 6.57e+00
  angle pdb=" C   GLN J 178 "
        pdb=" N   SER J 179 "
        pdb=" CA  SER J 179 "
      ideal   model   delta    sigma   weight residual
     120.60  124.62   -4.02 1.60e+00 3.91e-01 6.30e+00
  ... (remaining 15119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 6067
       17.58 -    35.16: 464
       35.16 -    52.74: 83
       52.74 -    70.31: 16
       70.31 -    87.89: 10
  Dihedral angle restraints: 6640
    sinusoidal: 2530
      harmonic: 4110
  Sorted by residual:
  dihedral pdb=" CB  CYS A  23 "
           pdb=" SG  CYS A  23 "
           pdb=" SG  CYS A  96 "
           pdb=" CB  CYS A  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.38   43.62     1      1.00e+01 1.00e-02 2.65e+01
  dihedral pdb=" CA  GLN J 178 "
           pdb=" C   GLN J 178 "
           pdb=" N   SER J 179 "
           pdb=" CA  SER J 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.50  -25.50     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CB  CYS K 135 "
           pdb=" SG  CYS K 135 "
           pdb=" SG  CYS K 195 "
           pdb=" CB  CYS K 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.90  -41.90     1      1.00e+01 1.00e-02 2.46e+01
  ... (remaining 6637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1048
       0.034 -    0.067: 428
       0.067 -    0.101: 158
       0.101 -    0.135: 58
       0.135 -    0.168: 8
  Chirality restraints: 1700
  Sorted by residual:
  chirality pdb=" CB  THR K  10 "
            pdb=" CA  THR K  10 "
            pdb=" OG1 THR K  10 "
            pdb=" CG2 THR K  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CG  LEU A  19 "
            pdb=" CB  LEU A  19 "
            pdb=" CD1 LEU A  19 "
            pdb=" CD2 LEU A  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.53e-01
  chirality pdb=" CA  ILE B  48 "
            pdb=" N   ILE B  48 "
            pdb=" C   ILE B  48 "
            pdb=" CB  ILE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.94e-01
  ... (remaining 1697 not shown)

  Planarity restraints: 1933
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU J 155 "    0.064 5.00e-02 4.00e+02   9.74e-02 1.52e+01
        pdb=" N   PRO J 156 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO J 156 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO J 156 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  13 "    0.027 5.00e-02 4.00e+02   4.01e-02 2.58e+00
        pdb=" N   PRO H  14 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 152 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO H 153 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO H 153 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 153 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1930 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 239
        2.67 -     3.22: 10207
        3.22 -     3.78: 16757
        3.78 -     4.34: 23800
        4.34 -     4.90: 39668
  Nonbonded interactions: 90671
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 105 "
            pdb=" OH  TYR B 173 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OE2 GLU C 102 "
            pdb=" OH  TYR L  49 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" NE2 GLN J 178 "
            pdb=" OG  SER J 180 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   TYR K 187 "
            pdb=" OH  TYR K 193 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" NH1 ARG H  98 "
            pdb=" OD1 ASN H 108 "
     model   vdw
     2.204 3.120
  ... (remaining 90666 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 'B' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ 
 resid 14 through 28 or resid 31 or resid 33 through 36 or resid 38 through 45 o \ 
r resid 47 through 49 or resid 51 through 52 or resid 54 or resid 56 through 59  \ 
or resid 61 through 69 or resid 71 through 75 or resid 78 or resid 81 through 84 \ 
 or resid 86 or resid 88 or resid 90 or resid 95 or resid 97 through 99 or resid \ 
 101 through 104 or resid 106 through 210))
  selection = (chain 'K' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ 
 resid 14 through 28 or resid 31 or resid 34 through 37 or resid 39 through 46 o \ 
r resid 48 through 50 or resid 52 through 53 or resid 55 or resid 57 through 60  \ 
or resid 62 through 70 or resid 72 through 76 or resid 79 or resid 82 through 85 \ 
 or resid 87 or resid 89 or resid 91 or resid 96 or resid 98 through 100 or resi \ 
d 102 through 105 or resid 107 through 149 or resid 160 through 211))
  selection = (chain 'L' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ 
 resid 14 through 28 or resid 31 or resid 33 through 36 or resid 38 through 45 o \ 
r resid 47 through 49 or resid 51 through 52 or resid 54 or resid 56 through 59  \ 
or resid 61 through 69 or resid 71 through 75 or resid 78 or resid 81 through 84 \ 
 or resid 86 or resid 88 or resid 90 or resid 95 or resid 97 through 99 or resid \ 
 101 through 104 or resid 106 through 148 or resid 159 through 210))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.710
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11133  Z= 0.165
  Angle     :  0.613   7.625  15148  Z= 0.333
  Chirality :  0.045   0.168   1700
  Planarity :  0.005   0.097   1933
  Dihedral  : 13.075  87.893   3970
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.08 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.92 (0.22), residues: 1400
  helix: -0.59 (0.57), residues: 83
  sheet: -1.13 (0.20), residues: 646
  loop : -1.39 (0.24), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 158 
 HIS   0.003   0.001   HIS L  89 
 PHE   0.015   0.001   PHE A  79 
 TYR   0.019   0.001   TYR L 186 
 ARG   0.008   0.001   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12939 (  419)
  hydrogen bonds       : angle       7.58703 ( 1281)
  SS BOND              : bond        0.00359 (   12)
  SS BOND              : angle       0.95231 (   24)
  covalent geometry    : bond        0.00364 (11121)
  covalent geometry    : angle       0.61221 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: J  145 LEU cc_start: 0.8710 (mt) cc_final: 0.8461 (mt)
REVERT: J  152 TYR cc_start: 0.7908 (p90) cc_final: 0.7511 (p90)
REVERT: J  204 ASN cc_start: 0.7890 (p0) cc_final: 0.7489 (p0)
REVERT: K   80 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7866 (mt-10)
REVERT: K  140 PHE cc_start: 0.8928 (p90) cc_final: 0.8463 (p90)
REVERT: K  143 ARG cc_start: 0.8375 (ttt-90) cc_final: 0.7987 (tpt90)
REVERT: H   73 ASP cc_start: 0.8279 (t0) cc_final: 0.7849 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2870
  time to fit residues: 67.8702
Evaluate side-chains
  145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:   10.0000
   chunk 105 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 108 optimal weight:   10.0000
   chunk 42 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 126 optimal weight:   10.0000
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 159 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.109033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.067932 restraints weight = 20311.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 2.44
r_work: 0.2794 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084  11133  Z= 0.300
  Angle     :  0.651   8.241  15148  Z= 0.342
  Chirality :  0.046   0.166   1700
  Planarity :  0.005   0.077   1933
  Dihedral  :  4.981  70.901   1526
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.27 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.92 (0.22), residues: 1400
  helix: -0.41 (0.57), residues: 85
  sheet: -1.08 (0.19), residues: 651
  loop : -1.49 (0.24), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP K  97 
 HIS   0.005   0.001   HIS L  89 
 PHE   0.017   0.002   PHE H 128 
 TYR   0.021   0.002   TYR L  91 
 ARG   0.006   0.001   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  419)
  hydrogen bonds       : angle       6.11756 ( 1281)
  SS BOND              : bond        0.00378 (   12)
  SS BOND              : angle       1.03892 (   24)
  covalent geometry    : bond        0.00697 (11121)
  covalent geometry    : angle       0.64983 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 161
  time to evaluate  : 2.952 
Fit side-chains
REVERT: B  105 ASP cc_start: 0.7427 (t0) cc_final: 0.7200 (t0)
REVERT: C   76 ASP cc_start: 0.8532 (t0) cc_final: 0.8275 (t0)
REVERT: J   43 GLN cc_start: 0.8652 (mm110) cc_final: 0.8447 (mm110)
REVERT: J  145 LEU cc_start: 0.8723 (mt) cc_final: 0.8485 (mt)
REVERT: J  152 TYR cc_start: 0.8350 (p90) cc_final: 0.7933 (p90)
REVERT: K   78 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7461 (mmm-85)
REVERT: K   80 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8054 (mm-30)
REVERT: K  143 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8121 (tpt90)
REVERT: L   24 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7590 (mmm160)
REVERT: L  142 ARG cc_start: 0.8355 (tpt90) cc_final: 0.8050 (tpt90)
REVERT: L  158 ASN cc_start: 0.8942 (p0) cc_final: 0.8729 (p0)
REVERT: L  211 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7460 (ttp-110)
REVERT: H    6 GLU cc_start: 0.8864 (mp0) cc_final: 0.8661 (mp0)
REVERT: H   73 ASP cc_start: 0.8671 (t0) cc_final: 0.8278 (t70)
REVERT: H   77 LYS cc_start: 0.8804 (mttt) cc_final: 0.8598 (mttt)
  outliers start: 12
  outliers final: 10
  residues processed: 168
  average time/residue: 0.3072
  time to fit residues: 69.7959
Evaluate side-chains
  159 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 GLN
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 119 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 115 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 ASN
J 178 GLN
K 161 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 210 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.111940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.071437 restraints weight = 20653.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.41
r_work: 0.2876 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11133  Z= 0.131
  Angle     :  0.561   6.985  15148  Z= 0.292
  Chirality :  0.044   0.151   1700
  Planarity :  0.005   0.083   1933
  Dihedral  :  4.820  70.976   1526
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  9.72 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.63 (0.22), residues: 1400
  helix: -0.06 (0.59), residues: 85
  sheet: -0.85 (0.20), residues: 640
  loop : -1.36 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  35 
 HIS   0.002   0.001   HIS L  89 
 PHE   0.014   0.001   PHE H 128 
 TYR   0.015   0.001   TYR K  92 
 ARG   0.006   0.000   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03080 (  419)
  hydrogen bonds       : angle       5.62706 ( 1281)
  SS BOND              : bond        0.00259 (   12)
  SS BOND              : angle       0.98110 (   24)
  covalent geometry    : bond        0.00300 (11121)
  covalent geometry    : angle       0.55993 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: C   76 ASP cc_start: 0.8528 (t0) cc_final: 0.8139 (t0)
REVERT: J  145 LEU cc_start: 0.8744 (mt) cc_final: 0.8488 (mt)
REVERT: J  152 TYR cc_start: 0.8361 (p90) cc_final: 0.7947 (p90)
REVERT: K  143 ARG cc_start: 0.8616 (ttt-90) cc_final: 0.8289 (tpt90)
REVERT: K  168 ASP cc_start: 0.8336 (t0) cc_final: 0.8076 (t0)
REVERT: K  174 TYR cc_start: 0.7125 (m-10) cc_final: 0.6917 (m-10)
REVERT: K  193 TYR cc_start: 0.6662 (m-10) cc_final: 0.6388 (m-80)
REVERT: L   24 ARG cc_start: 0.8011 (mtp-110) cc_final: 0.7677 (mmm160)
REVERT: L  134 CYS cc_start: 0.7553 (t) cc_final: 0.7114 (t)
REVERT: L  142 ARG cc_start: 0.8350 (tpt90) cc_final: 0.8043 (tpt90)
REVERT: L  189 HIS cc_start: 0.8215 (m170) cc_final: 0.7976 (m170)
REVERT: L  210 ASN cc_start: 0.8384 (m-40) cc_final: 0.8033 (m-40)
REVERT: H   73 ASP cc_start: 0.8614 (t0) cc_final: 0.8253 (t70)
  outliers start: 16
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2573
  time to fit residues: 60.6138
Evaluate side-chains
  155 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 GLN
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0040
   chunk 88 optimal weight:    0.0770
   chunk 91 optimal weight:    9.9990
   chunk 129 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   overall best weight:    2.4156

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 161 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 161 ASN
H 177 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.110182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.069566 restraints weight = 20237.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.36
r_work: 0.2828 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  11133  Z= 0.219
  Angle     :  0.592   7.424  15148  Z= 0.308
  Chirality :  0.044   0.156   1700
  Planarity :  0.005   0.087   1933
  Dihedral  :  4.797  70.690   1526
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.52 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.58 (0.22), residues: 1400
  helix: -0.09 (0.60), residues: 85
  sheet: -0.79 (0.20), residues: 650
  loop : -1.35 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP J 161 
 HIS   0.005   0.001   HIS L  89 
 PHE   0.015   0.002   PHE A  79 
 TYR   0.019   0.002   TYR L 140 
 ARG   0.006   0.000   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 (  419)
  hydrogen bonds       : angle       5.55282 ( 1281)
  SS BOND              : bond        0.00284 (   12)
  SS BOND              : angle       0.91250 (   24)
  covalent geometry    : bond        0.00509 (11121)
  covalent geometry    : angle       0.59127 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   76 ASP cc_start: 0.8566 (t0) cc_final: 0.8100 (t0)
REVERT: J  145 LEU cc_start: 0.8716 (mt) cc_final: 0.8489 (mt)
REVERT: J  152 TYR cc_start: 0.8349 (p90) cc_final: 0.7924 (p90)
REVERT: K  168 ASP cc_start: 0.8490 (t0) cc_final: 0.8110 (t0)
REVERT: L   24 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7677 (mmm160)
REVERT: L  134 CYS cc_start: 0.7780 (t) cc_final: 0.7408 (t)
REVERT: L  142 ARG cc_start: 0.8404 (tpt90) cc_final: 0.8121 (tpt90)
REVERT: L  158 ASN cc_start: 0.8944 (p0) cc_final: 0.8693 (p0)
REVERT: L  210 ASN cc_start: 0.8304 (m-40) cc_final: 0.7997 (m-40)
REVERT: H   73 ASP cc_start: 0.8632 (t0) cc_final: 0.8255 (t70)
  outliers start: 28
  outliers final: 18
  residues processed: 174
  average time/residue: 0.2858
  time to fit residues: 68.5136
Evaluate side-chains
  161 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 134 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0670
   chunk 126 optimal weight:    7.9990
   chunk 96 optimal weight:   30.0000
   chunk 137 optimal weight:   20.0000
   chunk 89 optimal weight:    8.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    2.5722

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.109975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.068939 restraints weight = 20520.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.38
r_work: 0.2827 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  11133  Z= 0.228
  Angle     :  0.598   7.846  15148  Z= 0.313
  Chirality :  0.045   0.153   1700
  Planarity :  0.005   0.090   1933
  Dihedral  :  4.841  70.549   1526
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.40 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.51 (0.22), residues: 1400
  helix:  0.05 (0.60), residues: 83
  sheet: -0.78 (0.20), residues: 650
  loop : -1.28 (0.24), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP J 161 
 HIS   0.005   0.001   HIS L  89 
 PHE   0.016   0.002   PHE A  79 
 TYR   0.022   0.002   TYR L 140 
 ARG   0.008   0.001   ARG K  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03235 (  419)
  hydrogen bonds       : angle       5.51669 ( 1281)
  SS BOND              : bond        0.00313 (   12)
  SS BOND              : angle       0.88290 (   24)
  covalent geometry    : bond        0.00529 (11121)
  covalent geometry    : angle       0.59751 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 1.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   76 ASP cc_start: 0.8525 (t0) cc_final: 0.8004 (t0)
REVERT: J  145 LEU cc_start: 0.8732 (mt) cc_final: 0.8501 (mt)
REVERT: J  152 TYR cc_start: 0.8369 (p90) cc_final: 0.7936 (p90)
REVERT: K  117 PHE cc_start: 0.8301 (m-80) cc_final: 0.7854 (m-80)
REVERT: K  143 ARG cc_start: 0.8502 (ttt-90) cc_final: 0.8184 (tpt90)
REVERT: K  168 ASP cc_start: 0.8661 (t0) cc_final: 0.8244 (t0)
REVERT: L   24 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7674 (mmm160)
REVERT: L  134 CYS cc_start: 0.7637 (t) cc_final: 0.7289 (t)
REVERT: L  142 ARG cc_start: 0.8421 (tpt90) cc_final: 0.8147 (tpt90)
REVERT: L  158 ASN cc_start: 0.8896 (p0) cc_final: 0.8601 (p0)
REVERT: L  187 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7642 (mm-30)
REVERT: L  199 GLN cc_start: 0.8478 (tt0) cc_final: 0.8277 (pt0)
REVERT: L  210 ASN cc_start: 0.8283 (m-40) cc_final: 0.8031 (m-40)
REVERT: L  211 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6833 (mtm180)
REVERT: H   73 ASP cc_start: 0.8640 (t0) cc_final: 0.8235 (t70)
REVERT: H   89 GLU cc_start: 0.8998 (pm20) cc_final: 0.8692 (pp20)
  outliers start: 27
  outliers final: 21
  residues processed: 172
  average time/residue: 0.4114
  time to fit residues: 99.5261
Evaluate side-chains
  161 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 1.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain L residue  211 ARG
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 137 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 130 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 111 optimal weight:    9.9990
   chunk 131 optimal weight:    7.9990
   chunk 122 optimal weight:    1.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.108357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.067295 restraints weight = 20652.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.37
r_work: 0.2794 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2665 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082  11133  Z= 0.288
  Angle     :  0.640   9.462  15148  Z= 0.334
  Chirality :  0.046   0.180   1700
  Planarity :  0.005   0.093   1933
  Dihedral  :  4.961  70.314   1526
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.46 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.61 (0.22), residues: 1400
  helix:  0.05 (0.60), residues: 83
  sheet: -0.89 (0.19), residues: 668
  loop : -1.29 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP K  97 
 HIS   0.006   0.001   HIS L  89 
 PHE   0.018   0.002   PHE C  63 
 TYR   0.024   0.002   TYR L 140 
 ARG   0.008   0.001   ARG K  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03450 (  419)
  hydrogen bonds       : angle       5.57444 ( 1281)
  SS BOND              : bond        0.00317 (   12)
  SS BOND              : angle       0.92073 (   24)
  covalent geometry    : bond        0.00670 (11121)
  covalent geometry    : angle       0.63922 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.6433 (tmt170) cc_final: 0.5820 (tmt170)
REVERT: C   76 ASP cc_start: 0.8559 (t0) cc_final: 0.7987 (t0)
REVERT: J    1 GLN cc_start: 0.8681 (pm20) cc_final: 0.8415 (pm20)
REVERT: J  145 LEU cc_start: 0.8748 (mt) cc_final: 0.8527 (mt)
REVERT: J  152 TYR cc_start: 0.8394 (p90) cc_final: 0.7946 (p90)
REVERT: J  189 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8158 (m)
REVERT: K  117 PHE cc_start: 0.8340 (m-80) cc_final: 0.7865 (m-80)
REVERT: K  143 ARG cc_start: 0.8474 (ttt-90) cc_final: 0.8165 (tpt90)
REVERT: K  168 ASP cc_start: 0.8755 (t0) cc_final: 0.8260 (t0)
REVERT: L   24 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7720 (mmm160)
REVERT: L  123 GLU cc_start: 0.8282 (pm20) cc_final: 0.7987 (pm20)
REVERT: L  142 ARG cc_start: 0.8448 (tpt90) cc_final: 0.8183 (tpt90)
REVERT: L  158 ASN cc_start: 0.8898 (p0) cc_final: 0.8554 (p0)
REVERT: L  210 ASN cc_start: 0.8322 (m-40) cc_final: 0.7989 (m-40)
REVERT: H   73 ASP cc_start: 0.8627 (t0) cc_final: 0.8240 (t70)
  outliers start: 30
  outliers final: 21
  residues processed: 171
  average time/residue: 0.3636
  time to fit residues: 85.7713
Evaluate side-chains
  161 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain J residue  189 VAL
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 28 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 130 optimal weight:    8.9990
   chunk 138 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** 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 = 0.3664 r_free = 0.3664 target = 0.110896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.070390 restraints weight = 20574.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.41
r_work: 0.2854 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11133  Z= 0.147
  Angle     :  0.582   8.479  15148  Z= 0.301
  Chirality :  0.044   0.166   1700
  Planarity :  0.005   0.092   1933
  Dihedral  :  4.804  70.652   1526
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.79 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.35 (0.22), residues: 1400
  helix:  0.13 (0.60), residues: 85
  sheet: -0.62 (0.20), residues: 643
  loop : -1.22 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP J 161 
 HIS   0.004   0.001   HIS L  89 
 PHE   0.015   0.001   PHE H 128 
 TYR   0.021   0.001   TYR H 151 
 ARG   0.008   0.000   ARG K  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03021 (  419)
  hydrogen bonds       : angle       5.33441 ( 1281)
  SS BOND              : bond        0.00266 (   12)
  SS BOND              : angle       0.76678 (   24)
  covalent geometry    : bond        0.00339 (11121)
  covalent geometry    : angle       0.58123 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 1.819 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.6523 (tmt170) cc_final: 0.5965 (tmt170)
REVERT: C   76 ASP cc_start: 0.8522 (t0) cc_final: 0.7997 (t0)
REVERT: J   43 GLN cc_start: 0.8539 (mm110) cc_final: 0.8325 (mm110)
REVERT: J  145 LEU cc_start: 0.8702 (mt) cc_final: 0.8473 (mt)
REVERT: J  152 TYR cc_start: 0.8370 (p90) cc_final: 0.7972 (p90)
REVERT: K  140 PHE cc_start: 0.8706 (p90) cc_final: 0.8390 (p90)
REVERT: K  143 ARG cc_start: 0.8509 (ttt-90) cc_final: 0.8248 (tpt90)
REVERT: K  168 ASP cc_start: 0.8736 (t0) cc_final: 0.8250 (t0)
REVERT: K  180 LEU cc_start: 0.8332 (tp) cc_final: 0.7829 (mt)
REVERT: L   24 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7668 (mmm160)
REVERT: L  142 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8149 (tpt90)
REVERT: L  158 ASN cc_start: 0.8902 (p0) cc_final: 0.8615 (p0)
REVERT: L  199 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8416 (pt0)
REVERT: L  210 ASN cc_start: 0.8241 (m-40) cc_final: 0.7992 (m-40)
REVERT: H   73 ASP cc_start: 0.8622 (t0) cc_final: 0.8231 (t70)
REVERT: H   89 GLU cc_start: 0.8964 (pm20) cc_final: 0.8708 (pp20)
REVERT: H  123 LYS cc_start: 0.8170 (tttm) cc_final: 0.7832 (tmtt)
  outliers start: 25
  outliers final: 20
  residues processed: 167
  average time/residue: 0.3617
  time to fit residues: 83.8087
Evaluate side-chains
  163 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain L residue  199 GLN
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 77 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9980
   chunk 134 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.110996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.070648 restraints weight = 20351.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 2.37
r_work: 0.2861 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11133  Z= 0.147
  Angle     :  0.579   8.342  15148  Z= 0.299
  Chirality :  0.044   0.153   1700
  Planarity :  0.005   0.095   1933
  Dihedral  :  4.712  70.762   1526
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.14 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.03 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.24 (0.22), residues: 1400
  helix:  0.32 (0.61), residues: 83
  sheet: -0.54 (0.20), residues: 643
  loop : -1.17 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP J 161 
 HIS   0.004   0.001   HIS L  89 
 PHE   0.017   0.001   PHE H 128 
 TYR   0.019   0.001   TYR L 140 
 ARG   0.009   0.001   ARG K  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02983 (  419)
  hydrogen bonds       : angle       5.24765 ( 1281)
  SS BOND              : bond        0.00302 (   12)
  SS BOND              : angle       0.78020 (   24)
  covalent geometry    : bond        0.00339 (11121)
  covalent geometry    : angle       0.57862 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.6531 (tmt170) cc_final: 0.6017 (tmt170)
REVERT: C   76 ASP cc_start: 0.8523 (t0) cc_final: 0.7993 (t0)
REVERT: J  145 LEU cc_start: 0.8646 (mt) cc_final: 0.8413 (mt)
REVERT: J  152 TYR cc_start: 0.8318 (p90) cc_final: 0.7965 (p90)
REVERT: K  117 PHE cc_start: 0.8405 (m-80) cc_final: 0.8067 (m-80)
REVERT: K  140 PHE cc_start: 0.8722 (p90) cc_final: 0.8500 (p90)
REVERT: K  143 ARG cc_start: 0.8504 (ttt-90) cc_final: 0.8259 (tpt90)
REVERT: K  168 ASP cc_start: 0.8746 (t0) cc_final: 0.8252 (t0)
REVERT: L   24 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7670 (mmm160)
REVERT: L  123 GLU cc_start: 0.8237 (pm20) cc_final: 0.7966 (pm20)
REVERT: L  142 ARG cc_start: 0.8397 (tpt90) cc_final: 0.8156 (tpt90)
REVERT: L  158 ASN cc_start: 0.8882 (p0) cc_final: 0.8582 (p0)
REVERT: L  199 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8409 (pt0)
REVERT: L  210 ASN cc_start: 0.8254 (m-40) cc_final: 0.8012 (m-40)
REVERT: H   73 ASP cc_start: 0.8626 (t0) cc_final: 0.8261 (t70)
REVERT: H   89 GLU cc_start: 0.8954 (pm20) cc_final: 0.8720 (pp20)
  outliers start: 29
  outliers final: 21
  residues processed: 165
  average time/residue: 0.3197
  time to fit residues: 73.6469
Evaluate side-chains
  162 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain L residue  199 GLN
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 132 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0020
   chunk 96 optimal weight:   20.0000
   chunk 73 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0870
   chunk 111 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    3.4172

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

Flipped N/Q/H residues before XYZ refinement:
K 125 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.108642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.067391 restraints weight = 20630.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 2.45
r_work: 0.2795 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2666 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.078  11133  Z= 0.284
  Angle     :  0.643   8.201  15148  Z= 0.335
  Chirality :  0.045   0.185   1700
  Planarity :  0.005   0.098   1933
  Dihedral  :  4.891  70.529   1526
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.21 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.69 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.39 (0.22), residues: 1400
  helix:  0.04 (0.59), residues: 85
  sheet: -0.66 (0.20), residues: 653
  loop : -1.22 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 158 
 HIS   0.006   0.001   HIS L  89 
 PHE   0.019   0.002   PHE H 128 
 TYR   0.028   0.002   TYR L 140 
 ARG   0.009   0.001   ARG K  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  419)
  hydrogen bonds       : angle       5.42360 ( 1281)
  SS BOND              : bond        0.00327 (   12)
  SS BOND              : angle       0.87656 (   24)
  covalent geometry    : bond        0.00660 (11121)
  covalent geometry    : angle       0.64288 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 2.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.6604 (tmt170) cc_final: 0.6136 (tmt170)
REVERT: C   76 ASP cc_start: 0.8582 (t0) cc_final: 0.8020 (t0)
REVERT: J  145 LEU cc_start: 0.8623 (mt) cc_final: 0.8406 (mt)
REVERT: J  152 TYR cc_start: 0.8360 (p90) cc_final: 0.7993 (p90)
REVERT: K  117 PHE cc_start: 0.8455 (m-80) cc_final: 0.8093 (m-80)
REVERT: K  143 ARG cc_start: 0.8500 (ttt-90) cc_final: 0.8180 (tpt90)
REVERT: K  168 ASP cc_start: 0.8787 (t0) cc_final: 0.8271 (t0)
REVERT: L   24 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7779 (mmm160)
REVERT: L  140 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7842 (t80)
REVERT: L  158 ASN cc_start: 0.8873 (p0) cc_final: 0.8515 (p0)
REVERT: L  199 GLN cc_start: 0.8744 (pt0) cc_final: 0.8495 (pt0)
REVERT: L  210 ASN cc_start: 0.8284 (m-40) cc_final: 0.8035 (m-40)
REVERT: H   73 ASP cc_start: 0.8619 (t0) cc_final: 0.8226 (t70)
REVERT: H   89 GLU cc_start: 0.8987 (pm20) cc_final: 0.8733 (pp20)
REVERT: H  123 LYS cc_start: 0.8198 (tttm) cc_final: 0.7921 (tmtt)
  outliers start: 23
  outliers final: 21
  residues processed: 162
  average time/residue: 0.4914
  time to fit residues: 111.6901
Evaluate side-chains
  160 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  140 TYR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 125 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 132 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 6 optimal weight:    0.1980
   chunk 121 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 112 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
J  43 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.112517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.072059 restraints weight = 20435.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.43
r_work: 0.2887 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11133  Z= 0.121
  Angle     :  0.589   8.355  15148  Z= 0.303
  Chirality :  0.044   0.174   1700
  Planarity :  0.005   0.095   1933
  Dihedral  :  4.711  70.877   1526
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.79 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.85 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.16 (0.23), residues: 1400
  helix:  0.26 (0.60), residues: 85
  sheet: -0.42 (0.20), residues: 628
  loop : -1.17 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  48 
 HIS   0.004   0.001   HIS L  89 
 PHE   0.020   0.001   PHE H 128 
 TYR   0.018   0.001   TYR L 140 
 ARG   0.011   0.001   ARG K  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02861 (  419)
  hydrogen bonds       : angle       5.17434 ( 1281)
  SS BOND              : bond        0.00276 (   12)
  SS BOND              : angle       0.73557 (   24)
  covalent geometry    : bond        0.00273 (11121)
  covalent geometry    : angle       0.58899 (15124)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.6661 (tmt170) cc_final: 0.6185 (tmt170)
REVERT: C   76 ASP cc_start: 0.8509 (t0) cc_final: 0.7982 (t0)
REVERT: J  145 LEU cc_start: 0.8653 (mt) cc_final: 0.8420 (mt)
REVERT: J  152 TYR cc_start: 0.8316 (p90) cc_final: 0.7960 (p90)
REVERT: K  117 PHE cc_start: 0.8520 (m-80) cc_final: 0.8227 (m-80)
REVERT: K  143 ARG cc_start: 0.8509 (ttt-90) cc_final: 0.8267 (tpt90)
REVERT: K  168 ASP cc_start: 0.8738 (t0) cc_final: 0.8188 (t0)
REVERT: L   24 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7695 (mmm160)
REVERT: L  158 ASN cc_start: 0.8834 (p0) cc_final: 0.8592 (p0)
REVERT: L  199 GLN cc_start: 0.8759 (pt0) cc_final: 0.8531 (pt0)
REVERT: L  210 ASN cc_start: 0.8218 (m-40) cc_final: 0.7996 (m-40)
REVERT: H   73 ASP cc_start: 0.8625 (t0) cc_final: 0.8247 (t70)
REVERT: H   89 GLU cc_start: 0.8961 (pm20) cc_final: 0.8728 (pp20)
REVERT: H  123 LYS cc_start: 0.8216 (tttm) cc_final: 0.7918 (tmtt)
  outliers start: 22
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2551
  time to fit residues: 57.2354
Evaluate side-chains
  156 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  148 TRP
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain J residue   91 THR
Chi-restraints excluded: chain K residue   10 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue  197 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  167 ASP
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  204 VAL
Chi-restraints excluded: chain H residue  213 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 129 optimal weight:    0.0970
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:   20.0000
   chunk 21 optimal weight:    7.9990
   chunk 108 optimal weight:    0.0980
   chunk 26 optimal weight:    6.9990
   overall best weight:    2.4384

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.109725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.069097 restraints weight = 20409.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.37
r_work: 0.2830 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  11133  Z= 0.222
  Angle     :  0.620   7.734  15148  Z= 0.323
  Chirality :  0.045   0.176   1700
  Planarity :  0.005   0.097   1933
  Dihedral  :  4.791  70.849   1526
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.57 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.58 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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: -1.23 (0.23), residues: 1400
  helix:  0.12 (0.59), residues: 85
  sheet: -0.51 (0.20), residues: 641
  loop : -1.17 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 158 
 HIS   0.006   0.001   HIS L  89 
 PHE   0.021   0.002   PHE H 128 
 TYR   0.019   0.002   TYR L 140 
 ARG   0.008   0.001   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03149 (  419)
  hydrogen bonds       : angle       5.28034 ( 1281)
  SS BOND              : bond        0.00275 (   12)
  SS BOND              : angle       0.80941 (   24)
  covalent geometry    : bond        0.00520 (11121)
  covalent geometry    : angle       0.61998 (15124)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8917.49 seconds
wall clock time: 165 minutes 6.52 seconds (9906.52 seconds total)