Starting phenix.real_space_refine
on Sat Aug 23 13:00:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uhf_42279/08_2025/8uhf_42279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uhf_42279/08_2025/8uhf_42279.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uhf_42279/08_2025/8uhf_42279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uhf_42279/08_2025/8uhf_42279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uhf_42279/08_2025/8uhf_42279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uhf_42279/08_2025/8uhf_42279.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.121 sd=   0.873
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      61      5.16       5
     C    7833      2.51       5
     N    2083      2.21       5
     O    2434      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12411
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1369
          Classifications: {'peptide': 192}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 186}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1413
          Classifications: {'peptide': 198}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 191}
    Chain: "C"
      Number of atoms: 1413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1413
          Classifications: {'peptide': 198}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 191}
    Chain: "D"
      Number of atoms: 1369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1369
          Classifications: {'peptide': 192}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 186}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1358
          Classifications: {'peptide': 190}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 184}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1370
          Classifications: {'peptide': 192}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 186}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1413
          Classifications: {'peptide': 198}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 191}
    Chain: "H"
      Number of atoms: 1345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1345
          Classifications: {'peptide': 188}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 182}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1361
          Classifications: {'peptide': 191}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 185}
          Chain breaks: 1
  Time building chain proxies: 3.50, per 1000 atoms: 0.28
  Number of scatterers: 12411
  At special positions: 0
  Unit cell: (96.28, 96.28, 158.53, 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      61     16.00
     O    2434      8.00
     N    2083      7.00
     C    7833      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 120 " - pdb=" SG  CYS A 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 120 " - pdb=" SG  CYS C 186 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 120 " - pdb=" SG  CYS D 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 120 " - pdb=" SG  CYS E 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 120 " - pdb=" SG  CYS F 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 120 " - pdb=" SG  CYS G 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 120 " - pdb=" SG  CYS H 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 120 " - pdb=" SG  CYS I 186 " 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: 0.93
  Conformation dependent library (CDL) restraints added in 602.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3168

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 9 sheets defined
      45.1% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 10
    Processing helix  chain 'A' and resid 19 through 51
      removed outlier: 4.120A  pdb=" N   SER A  42 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ILE A  43 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 76
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 116 through 127
    Processing helix  chain 'A' and resid 178 through 185
    Processing helix  chain 'B' and resid 3 through 10
      removed outlier: 3.525A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 51
      removed outlier: 3.571A  pdb=" N   SER B  17 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 76
    Processing helix  chain 'B' and resid 116 through 128
      removed outlier: 3.781A  pdb=" N   LYS B 121 " --> pdb=" O   GLN B 117 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   THR B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 185
    Processing helix  chain 'C' and resid 3 through 52
      removed outlier: 4.059A  pdb=" N   VAL C  20 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   VAL C  21 " --> pdb=" O   SER C  17 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR C  22 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN C  38 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 76
    Processing helix  chain 'C' and resid 116 through 128
    Processing helix  chain 'C' and resid 129 through 131
      No H-bonds generated for 'chain 'C' and resid 129 through 131'
    Processing helix  chain 'C' and resid 178 through 183
    Processing helix  chain 'D' and resid 4 through 11
    Processing helix  chain 'D' and resid 11 through 16
    Processing helix  chain 'D' and resid 19 through 51
      removed outlier: 4.081A  pdb=" N   LEU D  23 " --> pdb=" O   GLY D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 54
      No H-bonds generated for 'chain 'D' and resid 52 through 54'
    Processing helix  chain 'D' and resid 62 through 76
    Processing helix  chain 'D' and resid 81 through 85
    Processing helix  chain 'D' and resid 116 through 128
    Processing helix  chain 'D' and resid 178 through 184
    Processing helix  chain 'E' and resid 2 through 9
    Processing helix  chain 'E' and resid 11 through 51
    Processing helix  chain 'E' and resid 62 through 76
    Processing helix  chain 'E' and resid 116 through 128
    Processing helix  chain 'E' and resid 179 through 184
    Processing helix  chain 'F' and resid 3 through 51
      removed outlier: 3.646A  pdb=" N   ILE F   7 " --> pdb=" O   LEU F   3 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLY F  14 " --> pdb=" O   LEU F  10 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL F  15 " --> pdb=" O   GLY F  11 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL F  16 " --> pdb=" O   ILE F  12 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   SER F  17 " --> pdb=" O   MET F  13 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 76
    Processing helix  chain 'F' and resid 80 through 85
    Processing helix  chain 'F' and resid 116 through 128
    Processing helix  chain 'F' and resid 143 through 147
    Processing helix  chain 'F' and resid 178 through 184
    Processing helix  chain 'G' and resid 2 through 51
      removed outlier: 3.989A  pdb=" N   GLY G  19 " --> pdb=" O   VAL G  15 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   VAL G  21 " --> pdb=" O   SER G  17 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR G  22 " --> pdb=" O   ALA G  18 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG G  26 " --> pdb=" O   THR G  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 76
    Processing helix  chain 'G' and resid 80 through 85
    Processing helix  chain 'G' and resid 116 through 128
    Processing helix  chain 'G' and resid 178 through 184
      removed outlier: 3.562A  pdb=" N   VAL G 182 " --> pdb=" O   ASN G 178 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 3 through 49
      removed outlier: 3.580A  pdb=" N   ILE H   7 " --> pdb=" O   LEU H   3 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL H  15 " --> pdb=" O   GLY H  11 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   VAL H  16 " --> pdb=" O   ILE H  12 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 76
    Processing helix  chain 'H' and resid 80 through 85
    Processing helix  chain 'H' and resid 116 through 128
    Processing helix  chain 'H' and resid 178 through 184
    Processing helix  chain 'I' and resid 4 through 19
      removed outlier: 3.917A  pdb=" N   ILE I   8 " --> pdb=" O   LEU I   4 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 20 through 51
    Processing helix  chain 'I' and resid 63 through 76
    Processing helix  chain 'I' and resid 81 through 85
    Processing helix  chain 'I' and resid 116 through 128
    Processing helix  chain 'I' and resid 178 through 184
      removed outlier: 3.644A  pdb=" N   VAL I 182 " --> pdb=" O   ASN I 178 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97
      removed outlier: 6.176A  pdb=" N   PHE A 192 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 94 through 96
      removed outlier: 6.660A  pdb=" N   ILE B 134 " --> pdb=" O   ILE B 164 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 94 through 96
      removed outlier: 3.614A  pdb=" N   ASN C  94 " --> pdb=" O   SER C 111 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE C 134 " --> pdb=" O   ILE C 164 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 94 through 100
      removed outlier: 6.524A  pdb=" N   ARG D 100 " --> pdb=" O   ASN D 105 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ASN D 105 " --> pdb=" O   ARG D 100 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   SER D 111 " --> pdb=" O   PHE D 196 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   PHE D 196 " --> pdb=" O   SER D 111 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ASP D 113 " --> pdb=" O   VAL D 194 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL D 194 " --> pdb=" O   ASP D 113 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ILE D 134 " --> pdb=" O   ILE D 164 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 94 through 97
      removed outlier: 3.983A  pdb=" N   PHE E 108 " --> pdb=" O   ASN E 198 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ILE E 134 " --> pdb=" O   ILE E 164 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 94 through 98
      removed outlier: 3.729A  pdb=" N   ASN F  94 " --> pdb=" O   SER F 111 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA F 107 " --> pdb=" O   PHE F  98 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   ALA F 109 " --> pdb=" O   ASN F 198 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   ASN F 198 " --> pdb=" O   ALA F 109 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   SER F 111 " --> pdb=" O   PHE F 196 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   PHE F 196 " --> pdb=" O   SER F 111 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   ASP F 113 " --> pdb=" O   VAL F 194 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   VAL F 194 " --> pdb=" O   ASP F 113 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ILE F 134 " --> pdb=" O   ILE F 164 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 94 through 100
      removed outlier: 7.028A  pdb=" N   ARG G 100 " --> pdb=" O   ASN G 105 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ASN G 105 " --> pdb=" O   ARG G 100 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   PHE G 192 " --> pdb=" O   GLY G 114 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR G 133 " --> pdb=" O   GLY G 197 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE G 134 " --> pdb=" O   ILE G 164 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 94 through 100
      removed outlier: 7.078A  pdb=" N   ARG H 100 " --> pdb=" O   ASN H 105 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ASN H 105 " --> pdb=" O   ARG H 100 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE H 108 " --> pdb=" O   ASN H 198 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   PHE H 192 " --> pdb=" O   GLY H 114 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR H 133 " --> pdb=" O   GLY H 197 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ILE H 134 " --> pdb=" O   ILE H 164 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 94 through 98
      removed outlier: 3.510A  pdb=" N   ALA I 107 " --> pdb=" O   PHE I  98 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   ALA I 109 " --> pdb=" O   ASN I 198 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ASN I 198 " --> pdb=" O   ALA I 109 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   SER I 111 " --> pdb=" O   PHE I 196 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   PHE I 196 " --> pdb=" O   SER I 111 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ASP I 113 " --> pdb=" O   VAL I 194 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL I 194 " --> pdb=" O   ASP I 113 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR I 133 " --> pdb=" O   GLY I 197 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE I 134 " --> pdb=" O   ILE I 164 " (cutoff:3.500A)

    714 hydrogen bonds defined for protein.
    2043 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4098
        1.34 -     1.46: 2512
        1.46 -     1.58: 5823
        1.58 -     1.70: 0
        1.70 -     1.81: 104
  Bond restraints: 12537
  Sorted by residual:
  bond pdb=" CG  PRO G 191 "
       pdb=" CD  PRO G 191 "
    ideal  model  delta    sigma   weight residual
    1.512  1.487  0.025 2.70e-02 1.37e+03 8.45e-01
  bond pdb=" C   PHE A 131 "
       pdb=" O   PHE A 131 "
    ideal  model  delta    sigma   weight residual
    1.248  1.238  0.011 1.26e-02 6.30e+03 7.24e-01
  bond pdb=" CB  CYS E 120 "
       pdb=" SG  CYS E 120 "
    ideal  model  delta    sigma   weight residual
    1.808  1.781  0.027 3.30e-02 9.18e+02 6.89e-01
  bond pdb=" C   VAL D 127 "
       pdb=" O   VAL D 127 "
    ideal  model  delta    sigma   weight residual
    1.236  1.227  0.009 1.19e-02 7.06e+03 6.15e-01
  bond pdb=" CG  PRO E 191 "
       pdb=" CD  PRO E 191 "
    ideal  model  delta    sigma   weight residual
    1.512  1.491  0.021 2.70e-02 1.37e+03 5.96e-01
  ... (remaining 12532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 16801
        1.78 -     3.57: 172
        3.57 -     5.35: 21
        5.35 -     7.14: 6
        7.14 -     8.92: 1
  Bond angle restraints: 17001
  Sorted by residual:
  angle pdb=" CA  CYS C 120 "
        pdb=" CB  CYS C 120 "
        pdb=" SG  CYS C 120 "
      ideal   model   delta    sigma   weight residual
     114.40  123.32   -8.92 2.30e+00 1.89e-01 1.51e+01
  angle pdb=" N   ILE B   7 "
        pdb=" CA  ILE B   7 "
        pdb=" C   ILE B   7 "
      ideal   model   delta    sigma   weight residual
     112.80  108.83    3.97 1.15e+00 7.56e-01 1.19e+01
  angle pdb=" C   LEU C 185 "
        pdb=" N   CYS C 186 "
        pdb=" CA  CYS C 186 "
      ideal   model   delta    sigma   weight residual
     122.46  126.59   -4.13 1.41e+00 5.03e-01 8.56e+00
  angle pdb=" C   LEU A   3 "
        pdb=" N   LEU A   4 "
        pdb=" CA  LEU A   4 "
      ideal   model   delta    sigma   weight residual
     121.54  126.62   -5.08 1.91e+00 2.74e-01 7.08e+00
  angle pdb=" C   CYS C 120 "
        pdb=" CA  CYS C 120 "
        pdb=" CB  CYS C 120 "
      ideal   model   delta    sigma   weight residual
     110.84  106.92    3.92 1.66e+00 3.63e-01 5.56e+00
  ... (remaining 16996 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 7104
       17.91 -    35.81: 410
       35.81 -    53.72: 60
       53.72 -    71.63: 15
       71.63 -    89.53: 10
  Dihedral angle restraints: 7599
    sinusoidal: 2686
      harmonic: 4913
  Sorted by residual:
  dihedral pdb=" CB  CYS A 120 "
           pdb=" SG  CYS A 120 "
           pdb=" SG  CYS A 186 "
           pdb=" CB  CYS A 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.43   50.43     1      1.00e+01 1.00e-02 3.48e+01
  dihedral pdb=" CB  CYS C 120 "
           pdb=" SG  CYS C 120 "
           pdb=" SG  CYS C 186 "
           pdb=" CB  CYS C 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.75  -36.75     1      1.00e+01 1.00e-02 1.91e+01
  dihedral pdb=" CB  CYS I 120 "
           pdb=" SG  CYS I 120 "
           pdb=" SG  CYS I 186 "
           pdb=" CB  CYS I 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.56  -33.56     1      1.00e+01 1.00e-02 1.60e+01
  ... (remaining 7596 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1280
       0.026 -    0.052: 542
       0.052 -    0.078: 206
       0.078 -    0.105: 68
       0.105 -    0.131: 47
  Chirality restraints: 2143
  Sorted by residual:
  chirality pdb=" CA  ILE G 134 "
            pdb=" N   ILE G 134 "
            pdb=" C   ILE G 134 "
            pdb=" CB  ILE G 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  VAL E 112 "
            pdb=" N   VAL E 112 "
            pdb=" C   VAL E 112 "
            pdb=" CB  VAL E 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  ILE E 110 "
            pdb=" N   ILE E 110 "
            pdb=" C   ILE E 110 "
            pdb=" CB  ILE E 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 2140 not shown)

  Planarity restraints: 2174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A   4 "   -0.012 2.00e-02 2.50e+03   2.47e-02 6.10e+00
        pdb=" C   LEU A   4 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LEU A   4 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLU A   5 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D   9 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.86e+00
        pdb=" C   VAL D   9 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL D   9 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU D  10 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B   7 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.20e+00
        pdb=" C   ILE B   7 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ILE B   7 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B   8 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2171 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 232
        2.68 -     3.24: 12801
        3.24 -     3.79: 19679
        3.79 -     4.35: 25879
        4.35 -     4.90: 42002
  Nonbonded interactions: 100593
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  39 "
            pdb=" O   GLU B  83 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OG  SER A  39 "
            pdb=" O   GLU A  83 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER F  80 "
            pdb=" OD1 ASP F  82 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ASP H 149 "
            pdb=" OG  SER H 153 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   GLY E 128 "
            pdb=" NZ  LYS E 165 "
     model   vdw
     2.247 3.120
  ... (remaining 100588 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 52 or resid 62 through 196))
  selection = (chain 'B' and (resid 2 through 52 or resid 62 through 196))
  selection = (chain 'C' and (resid 2 through 52 or resid 62 through 196))
  selection = (chain 'D' and (resid 2 through 52 or resid 62 through 196))
  selection = (chain 'E' and (resid 2 through 52 or resid 62 through 196))
  selection = (chain 'F' and (resid 2 through 52 or resid 62 through 196))
  selection = (chain 'G' and (resid 2 through 52 or resid 62 through 196))
  selection = (chain 'H' and resid 2 through 196)
  selection = (chain 'I' and (resid 2 through 52 or resid 62 through 196))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  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:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.600
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12546  Z= 0.098
  Angle     :  0.497   8.924  17019  Z= 0.277
  Chirality :  0.038   0.131   2143
  Planarity :  0.003   0.029   2174
  Dihedral  : 12.209  89.532   4404
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.19), residues: 1709
  helix: -0.07 (0.18), residues: 733
  sheet: -0.81 (0.33), residues: 212
  loop : -1.95 (0.20), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  52 
 TYR   0.004   0.001   TYR G 133 
 PHE   0.008   0.001   PHE G 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 (12537)
  covalent geometry    : angle       0.49458 (17001)
  SS BOND              : bond        0.00255 (    9)
  SS BOND              : angle       1.43088 (   18)
  hydrogen bonds       : bond        0.16009 (  714)
  hydrogen bonds       : angle       6.39544 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 416
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  133 TYR cc_start: 0.8019 (t80) cc_final: 0.7722 (t80)
REVERT: B  165 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8277 (ttpp)
REVERT: B  175 ASP cc_start: 0.8310 (m-30) cc_final: 0.7924 (m-30)
REVERT: C   25 GLN cc_start: 0.8879 (tp40) cc_final: 0.8429 (tp40)
REVERT: C  120 CYS cc_start: 0.4546 (m) cc_final: 0.3447 (m)
REVERT: C  129 ASP cc_start: 0.9017 (p0) cc_final: 0.8644 (p0)
REVERT: C  131 PHE cc_start: 0.7036 (m-80) cc_final: 0.6806 (m-80)
REVERT: C  192 PHE cc_start: 0.5943 (m-80) cc_final: 0.4288 (m-10)
REVERT: D   13 MET cc_start: 0.8918 (mmm) cc_final: 0.8637 (mmm)
REVERT: D  129 ASP cc_start: 0.7319 (p0) cc_final: 0.7090 (p0)
REVERT: E  185 LEU cc_start: 0.8118 (tp) cc_final: 0.7899 (mt)
REVERT: F   62 ASP cc_start: 0.8566 (p0) cc_final: 0.8036 (p0)
REVERT: F   82 ASP cc_start: 0.8482 (p0) cc_final: 0.8265 (p0)
REVERT: F  159 THR cc_start: 0.8550 (p) cc_final: 0.8204 (p)
REVERT: F  196 PHE cc_start: 0.7544 (m-80) cc_final: 0.6994 (m-10)
REVERT: G    1 MET cc_start: 0.7122 (ttt) cc_final: 0.5623 (ttm)
REVERT: G   44 GLN cc_start: 0.8367 (tt0) cc_final: 0.8095 (tt0)
REVERT: G   49 GLN cc_start: 0.8771 (mm110) cc_final: 0.8530 (mm110)
REVERT: G   92 ASN cc_start: 0.8784 (m-40) cc_final: 0.8554 (m-40)
REVERT: G   96 PHE cc_start: 0.7090 (m-80) cc_final: 0.6864 (m-10)
REVERT: G  198 ASN cc_start: 0.6530 (m-40) cc_final: 0.5715 (m-40)
REVERT: H  131 PHE cc_start: 0.8685 (m-80) cc_final: 0.8296 (m-80)
REVERT: H  174 LEU cc_start: 0.9352 (tp) cc_final: 0.9078 (tt)
REVERT: I  183 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7280 (mt-10)
REVERT: I  196 PHE cc_start: 0.8626 (m-80) cc_final: 0.8397 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 416
  average time/residue: 0.1272
  time to fit residues: 70.4588
Evaluate side-chains
  283 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.1980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN
A  92 ASN
A 198 ASN
C  44 GLN
C 117 GLN
D  44 GLN
D  94 ASN
D 105 ASN
** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  49 GLN
G 101 ASN
H  41 ASN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 152 ASN
I  41 ASN
I  94 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.053189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.046080 restraints weight = 79945.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.047344 restraints weight = 47135.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.048201 restraints weight = 31318.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.048806 restraints weight = 22813.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.049232 restraints weight = 17800.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12546  Z= 0.132
  Angle     :  0.643  11.630  17019  Z= 0.335
  Chirality :  0.042   0.157   2143
  Planarity :  0.004   0.036   2174
  Dihedral  :  4.287  19.391   1773
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.64 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.20), residues: 1709
  helix:  0.95 (0.19), residues: 749
  sheet: -0.50 (0.32), residues: 222
  loop : -1.64 (0.20), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 100 
 TYR   0.016   0.002   TYR C 133 
 PHE   0.023   0.002   PHE E 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (12537)
  covalent geometry    : angle       0.64068 (17001)
  SS BOND              : bond        0.00696 (    9)
  SS BOND              : angle       1.83654 (   18)
  hydrogen bonds       : bond        0.03918 (  714)
  hydrogen bonds       : angle       5.26514 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 349
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8315 (mm110)
REVERT: A   41 ASN cc_start: 0.8348 (m-40) cc_final: 0.7972 (p0)
REVERT: A   93 MET cc_start: 0.6529 (mtt) cc_final: 0.6290 (mtt)
REVERT: A  137 LYS cc_start: 0.9203 (tptt) cc_final: 0.8897 (mppt)
REVERT: A  173 ASN cc_start: 0.8414 (t0) cc_final: 0.8058 (p0)
REVERT: B   33 MET cc_start: 0.8576 (mmm) cc_final: 0.8288 (mmm)
REVERT: B   93 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.6095 (mmp)
REVERT: B   94 ASN cc_start: 0.8230 (t0) cc_final: 0.7312 (t0)
REVERT: B   96 PHE cc_start: 0.7443 (m-80) cc_final: 0.6498 (m-10)
REVERT: C   33 MET cc_start: 0.8666 (tmm) cc_final: 0.8370 (tmm)
REVERT: C   78 LYS cc_start: 0.8318 (mmmm) cc_final: 0.7739 (mmmt)
REVERT: C  129 ASP cc_start: 0.8826 (p0) cc_final: 0.8569 (p0)
REVERT: C  192 PHE cc_start: 0.6434 (m-80) cc_final: 0.6176 (m-10)
REVERT: D   13 MET cc_start: 0.8731 (mmm) cc_final: 0.8318 (mmm)
REVERT: D  174 LEU cc_start: 0.9002 (mp) cc_final: 0.8709 (mp)
REVERT: E   25 GLN cc_start: 0.7775 (mt0) cc_final: 0.7364 (mt0)
REVERT: E   83 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8214 (tp30)
REVERT: F   44 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: F   62 ASP cc_start: 0.8525 (p0) cc_final: 0.8018 (p0)
REVERT: G   38 GLN cc_start: 0.8653 (tp40) cc_final: 0.8373 (tp-100)
REVERT: G   49 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8570 (mm110)
REVERT: G  101 ASN cc_start: 0.7392 (m-40) cc_final: 0.7177 (m-40)
REVERT: H   98 PHE cc_start: 0.7478 (p90) cc_final: 0.7138 (p90)
REVERT: H  174 LEU cc_start: 0.9277 (tp) cc_final: 0.9066 (tt)
REVERT: I   13 MET cc_start: 0.8118 (mmm) cc_final: 0.7781 (mtt)
REVERT: I  183 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7293 (mt-10)
REVERT: I  196 PHE cc_start: 0.8391 (m-80) cc_final: 0.7966 (m-10)
  outliers start: 14
  outliers final: 6
  residues processed: 355
  average time/residue: 0.1199
  time to fit residues: 58.6445
Evaluate side-chains
  291 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 284
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   92 ASN
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain I residue   78 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 108 optimal weight:    0.0670
   chunk 97 optimal weight:    9.9990
   chunk 166 optimal weight:   20.0000
   chunk 85 optimal weight:    6.9990
   chunk 118 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 157 optimal weight:    0.4980
   chunk 164 optimal weight:    9.9990
   chunk 155 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    3.5124

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
B  25 GLN
D  44 GLN
E 105 ASN
G 198 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  41 ASN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  92 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.050796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.043663 restraints weight = 83231.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.044865 restraints weight = 48268.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.045687 restraints weight = 32080.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.046255 restraints weight = 23491.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.046661 restraints weight = 18574.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12546  Z= 0.171
  Angle     :  0.666  11.993  17019  Z= 0.352
  Chirality :  0.042   0.188   2143
  Planarity :  0.004   0.039   2174
  Dihedral  :  4.624  20.133   1773
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 19.33 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.20), residues: 1709
  helix:  1.08 (0.19), residues: 754
  sheet: -0.17 (0.34), residues: 220
  loop : -1.41 (0.22), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 100 
 TYR   0.018   0.002   TYR C 133 
 PHE   0.034   0.002   PHE E 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (12537)
  covalent geometry    : angle       0.66184 (17001)
  SS BOND              : bond        0.00543 (    9)
  SS BOND              : angle       2.47204 (   18)
  hydrogen bonds       : bond        0.04261 (  714)
  hydrogen bonds       : angle       5.29696 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 311
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7816 (tptt)
REVERT: A   83 GLU cc_start: 0.7807 (pt0) cc_final: 0.7558 (pt0)
REVERT: A  137 LYS cc_start: 0.9122 (tptt) cc_final: 0.8875 (mppt)
REVERT: A  173 ASN cc_start: 0.8405 (t0) cc_final: 0.8036 (p0)
REVERT: B   94 ASN cc_start: 0.8242 (t0) cc_final: 0.7281 (t0)
REVERT: B   96 PHE cc_start: 0.7492 (m-80) cc_final: 0.6548 (m-10)
REVERT: C   78 LYS cc_start: 0.8292 (mmmm) cc_final: 0.7461 (tptp)
REVERT: C   91 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8394 (t)
REVERT: C  129 ASP cc_start: 0.8902 (p0) cc_final: 0.8651 (p0)
REVERT: C  196 PHE cc_start: 0.8487 (m-10) cc_final: 0.8279 (m-80)
REVERT: D  129 ASP cc_start: 0.7347 (p0) cc_final: 0.7083 (p0)
REVERT: E   68 LYS cc_start: 0.9103 (mttp) cc_final: 0.8755 (mmtp)
REVERT: E   83 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8435 (tp30)
REVERT: F   33 MET cc_start: 0.8293 (tpp) cc_final: 0.8078 (tpp)
REVERT: F   44 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: F   62 ASP cc_start: 0.8521 (p0) cc_final: 0.8053 (p0)
REVERT: F  100 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8408 (ttp80)
REVERT: G   38 GLN cc_start: 0.8684 (tp40) cc_final: 0.8394 (tp-100)
REVERT: G   49 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8582 (mm110)
REVERT: H   83 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7867 (tp30)
REVERT: I   13 MET cc_start: 0.8056 (mmm) cc_final: 0.7801 (mtm)
REVERT: I  183 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7274 (mt-10)
REVERT: I  196 PHE cc_start: 0.8452 (m-80) cc_final: 0.8022 (m-10)
  outliers start: 23
  outliers final: 10
  residues processed: 321
  average time/residue: 0.1088
  time to fit residues: 48.5001
Evaluate side-chains
  270 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 259
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   92 ASN
Chi-restraints excluded: chain B residue    3 LEU
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain E residue  187 LYS
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain I residue   92 ASN
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 17 optimal weight:   20.0000
   chunk 16 optimal weight:    0.0470
   chunk 151 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 118 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 130 optimal weight:    0.6980
   chunk 156 optimal weight:    0.0060
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
D  44 GLN
D  94 ASN
E  44 GLN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.052810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.045624 restraints weight = 80842.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.046851 restraints weight = 47687.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.047694 restraints weight = 31873.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.048297 restraints weight = 23332.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.048719 restraints weight = 18321.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12546  Z= 0.129
  Angle     :  0.639  12.221  17019  Z= 0.333
  Chirality :  0.041   0.142   2143
  Planarity :  0.003   0.035   2174
  Dihedral  :  4.411  21.013   1773
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.94 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.20), residues: 1709
  helix:  1.32 (0.19), residues: 757
  sheet:  0.08 (0.35), residues: 210
  loop : -1.30 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 100 
 TYR   0.013   0.001   TYR G  57 
 PHE   0.033   0.002   PHE C 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (12537)
  covalent geometry    : angle       0.63697 (17001)
  SS BOND              : bond        0.00993 (    9)
  SS BOND              : angle       1.73178 (   18)
  hydrogen bonds       : bond        0.03628 (  714)
  hydrogen bonds       : angle       5.06673 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 301
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7768 (tptt)
REVERT: A   83 GLU cc_start: 0.7794 (pt0) cc_final: 0.7545 (pt0)
REVERT: A  129 ASP cc_start: 0.8520 (m-30) cc_final: 0.8132 (m-30)
REVERT: A  137 LYS cc_start: 0.9042 (tptt) cc_final: 0.8827 (mppt)
REVERT: A  173 ASN cc_start: 0.8343 (t0) cc_final: 0.7985 (p0)
REVERT: B   94 ASN cc_start: 0.8237 (t0) cc_final: 0.7425 (t0)
REVERT: B   96 PHE cc_start: 0.7487 (m-80) cc_final: 0.6495 (m-10)
REVERT: B  123 LEU cc_start: 0.9546 (tp) cc_final: 0.9179 (pp)
REVERT: B  165 LYS cc_start: 0.8298 (ttpp) cc_final: 0.7990 (ptmm)
REVERT: C   78 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7415 (tptp)
REVERT: D   13 MET cc_start: 0.8655 (mmm) cc_final: 0.8420 (mmm)
REVERT: D  173 ASN cc_start: 0.8450 (m110) cc_final: 0.8197 (t0)
REVERT: E   68 LYS cc_start: 0.9112 (mttp) cc_final: 0.8905 (mmtp)
REVERT: E   83 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8341 (tp30)
REVERT: E  196 PHE cc_start: 0.7985 (m-10) cc_final: 0.7761 (m-80)
REVERT: F   44 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: F   62 ASP cc_start: 0.8569 (p0) cc_final: 0.8080 (p0)
REVERT: G   49 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8551 (mm110)
REVERT: H   83 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7880 (tp30)
REVERT: H  174 LEU cc_start: 0.9002 (tt) cc_final: 0.8297 (mp)
REVERT: I   13 MET cc_start: 0.8186 (mmm) cc_final: 0.7875 (mtt)
REVERT: I  183 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7252 (mt-10)
REVERT: I  196 PHE cc_start: 0.8443 (m-80) cc_final: 0.8016 (m-10)
  outliers start: 22
  outliers final: 7
  residues processed: 316
  average time/residue: 0.1096
  time to fit residues: 47.9402
Evaluate side-chains
  259 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 252
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   94 ASN
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   chunk 54 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 119 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 165 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9980
   chunk 169 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 73 optimal weight:   30.0000
   overall best weight:    3.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 105 ASN
A 119 GLN
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 GLN
D  94 ASN
D 117 GLN
E  44 GLN
G 101 ASN
G 173 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  92 ASN
** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.050315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.043288 restraints weight = 82775.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.044473 restraints weight = 48219.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.045277 restraints weight = 32048.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.045825 restraints weight = 23526.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.046200 restraints weight = 18625.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12546  Z= 0.184
  Angle     :  0.715  15.413  17019  Z= 0.374
  Chirality :  0.042   0.190   2143
  Planarity :  0.004   0.045   2174
  Dihedral  :  4.794  23.418   1773
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.47 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.20), residues: 1709
  helix:  1.15 (0.19), residues: 747
  sheet:  0.10 (0.35), residues: 216
  loop : -1.24 (0.22), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 100 
 TYR   0.012   0.002   TYR G  57 
 PHE   0.029   0.002   PHE E 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (12537)
  covalent geometry    : angle       0.70945 (17001)
  SS BOND              : bond        0.00745 (    9)
  SS BOND              : angle       2.75482 (   18)
  hydrogen bonds       : bond        0.04388 (  714)
  hydrogen bonds       : angle       5.29531 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 283
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7937 (mtm)
REVERT: A   83 GLU cc_start: 0.7800 (pt0) cc_final: 0.7556 (pt0)
REVERT: A  129 ASP cc_start: 0.8650 (m-30) cc_final: 0.8288 (m-30)
REVERT: A  137 LYS cc_start: 0.9119 (tptt) cc_final: 0.8841 (mppt)
REVERT: A  173 ASN cc_start: 0.8281 (t0) cc_final: 0.7933 (p0)
REVERT: B    1 MET cc_start: 0.8968 (tpp) cc_final: 0.8558 (tpp)
REVERT: B   25 GLN cc_start: 0.8316 (pt0) cc_final: 0.7957 (pt0)
REVERT: B  165 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7913 (ptmm)
REVERT: C   33 MET cc_start: 0.8660 (tmm) cc_final: 0.8320 (tmm)
REVERT: C   78 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7583 (tptp)
REVERT: D   13 MET cc_start: 0.8736 (mmm) cc_final: 0.8430 (mmm)
REVERT: E   83 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8408 (tp30)
REVERT: E   93 MET cc_start: 0.6924 (mtt) cc_final: 0.6693 (mtt)
REVERT: F   44 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: F   62 ASP cc_start: 0.8510 (p0) cc_final: 0.8026 (p0)
REVERT: G   38 GLN cc_start: 0.8653 (tp40) cc_final: 0.8369 (tp-100)
REVERT: G   49 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8578 (mm110)
REVERT: H   83 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7991 (tp30)
REVERT: H  129 ASP cc_start: 0.7479 (p0) cc_final: 0.6617 (p0)
REVERT: I   13 MET cc_start: 0.8209 (mmm) cc_final: 0.7889 (mtt)
REVERT: I   78 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8185 (mtmm)
REVERT: I   93 MET cc_start: 0.7824 (mmt) cc_final: 0.7579 (mmt)
REVERT: I  183 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: I  196 PHE cc_start: 0.8442 (m-80) cc_final: 0.7989 (m-10)
  outliers start: 31
  outliers final: 15
  residues processed: 305
  average time/residue: 0.1035
  time to fit residues: 44.2219
Evaluate side-chains
  271 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 255
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   33 MET
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   94 ASN
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue   92 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 140 optimal weight:    0.8980
   chunk 106 optimal weight:    6.9990
   chunk 165 optimal weight:    8.9990
   chunk 138 optimal weight:    9.9990
   chunk 100 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 83 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0270
   overall best weight:    3.3844

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

Flipped N/Q/H residues before XYZ refinement:
A 105 ASN
B  25 GLN
D  94 ASN
D 117 GLN
E  41 ASN
E  44 GLN
G  44 GLN
G  56 ASN
G 173 ASN
G 198 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.050358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.043383 restraints weight = 82629.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.044559 restraints weight = 48588.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.045364 restraints weight = 32350.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.045915 restraints weight = 23716.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.046313 restraints weight = 18713.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12546  Z= 0.173
  Angle     :  0.722  13.165  17019  Z= 0.375
  Chirality :  0.042   0.192   2143
  Planarity :  0.004   0.044   2174
  Dihedral  :  4.815  22.909   1773
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.31 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.20), residues: 1709
  helix:  1.08 (0.19), residues: 748
  sheet:  0.16 (0.35), residues: 216
  loop : -1.19 (0.23), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 100 
 TYR   0.013   0.002   TYR G  57 
 PHE   0.030   0.002   PHE C 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12537)
  covalent geometry    : angle       0.71804 (17001)
  SS BOND              : bond        0.00421 (    9)
  SS BOND              : angle       2.43010 (   18)
  hydrogen bonds       : bond        0.04249 (  714)
  hydrogen bonds       : angle       5.33264 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 276
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ASN cc_start: 0.8545 (m-40) cc_final: 0.8170 (m-40)
REVERT: A   83 GLU cc_start: 0.7854 (pt0) cc_final: 0.7634 (pt0)
REVERT: A  129 ASP cc_start: 0.8582 (m-30) cc_final: 0.8199 (m-30)
REVERT: A  137 LYS cc_start: 0.9115 (tptt) cc_final: 0.8863 (mppt)
REVERT: A  173 ASN cc_start: 0.8237 (t0) cc_final: 0.7963 (p0)
REVERT: B    1 MET cc_start: 0.8866 (tpp) cc_final: 0.8388 (tpp)
REVERT: B  131 PHE cc_start: 0.6860 (m-10) cc_final: 0.6641 (m-10)
REVERT: B  165 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7924 (ptmm)
REVERT: C   33 MET cc_start: 0.8695 (tmm) cc_final: 0.8342 (tmm)
REVERT: C   78 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7575 (tptp)
REVERT: D   13 MET cc_start: 0.8665 (mmm) cc_final: 0.8402 (mmm)
REVERT: D  100 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8188 (ttm110)
REVERT: E   62 ASP cc_start: 0.8267 (p0) cc_final: 0.8067 (p0)
REVERT: E  196 PHE cc_start: 0.8027 (m-10) cc_final: 0.7674 (m-80)
REVERT: F   44 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7680 (tm-30)
REVERT: F   62 ASP cc_start: 0.8474 (p0) cc_final: 0.7985 (p0)
REVERT: G    1 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7240 (ppp)
REVERT: G   38 GLN cc_start: 0.8691 (tp40) cc_final: 0.8387 (tp-100)
REVERT: G   49 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8557 (mm110)
REVERT: G  198 ASN cc_start: 0.6063 (m-40) cc_final: 0.5436 (m110)
REVERT: H   83 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7974 (tp30)
REVERT: H   98 PHE cc_start: 0.7353 (p90) cc_final: 0.7015 (p90)
REVERT: H  129 ASP cc_start: 0.7303 (p0) cc_final: 0.6910 (p0)
REVERT: H  130 MET cc_start: 0.6629 (mmm) cc_final: 0.6306 (mmm)
REVERT: H  174 LEU cc_start: 0.9342 (tp) cc_final: 0.9059 (tt)
REVERT: I   13 MET cc_start: 0.8274 (mmm) cc_final: 0.7839 (mmm)
REVERT: I   85 LYS cc_start: 0.9131 (mtmm) cc_final: 0.8911 (ptpp)
REVERT: I   93 MET cc_start: 0.7946 (mmt) cc_final: 0.7597 (mmt)
REVERT: I  183 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7343 (mt-10)
REVERT: I  196 PHE cc_start: 0.8462 (m-80) cc_final: 0.8030 (m-10)
  outliers start: 31
  outliers final: 18
  residues processed: 295
  average time/residue: 0.1193
  time to fit residues: 49.8527
Evaluate side-chains
  275 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 256
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain B residue    3 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   94 ASN
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  187 LYS
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain G residue    1 MET
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 151 optimal weight:    8.9990
   chunk 133 optimal weight:    0.3980
   chunk 92 optimal weight:    8.9990
   chunk 58 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 125 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   chunk 158 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    3.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 105 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 117 GLN
E  44 GLN
** E  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.050415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.043373 restraints weight = 83007.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.044554 restraints weight = 48824.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.045370 restraints weight = 32700.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.045919 restraints weight = 24072.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.046308 restraints weight = 19040.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12546  Z= 0.173
  Angle     :  0.731  12.742  17019  Z= 0.383
  Chirality :  0.043   0.196   2143
  Planarity :  0.004   0.055   2174
  Dihedral  :  4.854  23.213   1773
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 25.84 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.20), residues: 1709
  helix:  1.09 (0.19), residues: 743
  sheet:  0.19 (0.35), residues: 214
  loop : -1.20 (0.22), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 100 
 TYR   0.013   0.001   TYR G  51 
 PHE   0.031   0.002   PHE E 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12537)
  covalent geometry    : angle       0.72785 (17001)
  SS BOND              : bond        0.00369 (    9)
  SS BOND              : angle       2.31830 (   18)
  hydrogen bonds       : bond        0.04282 (  714)
  hydrogen bonds       : angle       5.35694 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 266
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASP cc_start: 0.8568 (m-30) cc_final: 0.8181 (m-30)
REVERT: A  137 LYS cc_start: 0.9114 (tptt) cc_final: 0.8893 (mppt)
REVERT: A  173 ASN cc_start: 0.8251 (t0) cc_final: 0.7944 (p0)
REVERT: B    1 MET cc_start: 0.8838 (tpp) cc_final: 0.8409 (tpp)
REVERT: B  165 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7921 (ptmm)
REVERT: C   33 MET cc_start: 0.8720 (tmm) cc_final: 0.8401 (tmm)
REVERT: C   78 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7554 (tptp)
REVERT: D   13 MET cc_start: 0.8604 (mmm) cc_final: 0.8378 (mmm)
REVERT: D   94 ASN cc_start: 0.8913 (m-40) cc_final: 0.8687 (m110)
REVERT: D  100 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8088 (ttm110)
REVERT: E    1 MET cc_start: 0.8347 (mpp) cc_final: 0.7495 (mpp)
REVERT: E   62 ASP cc_start: 0.8316 (p0) cc_final: 0.8028 (p0)
REVERT: E  196 PHE cc_start: 0.8077 (m-10) cc_final: 0.7805 (m-80)
REVERT: F   44 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: F   62 ASP cc_start: 0.8468 (p0) cc_final: 0.7968 (p0)
REVERT: G   38 GLN cc_start: 0.8680 (tp40) cc_final: 0.8367 (tp-100)
REVERT: G   49 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8488 (mm110)
REVERT: G  198 ASN cc_start: 0.6184 (m-40) cc_final: 0.5886 (m-40)
REVERT: H   83 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7882 (tp30)
REVERT: H   98 PHE cc_start: 0.7409 (p90) cc_final: 0.7017 (p90)
REVERT: H  100 ARG cc_start: 0.8364 (ptt90) cc_final: 0.7926 (ptp90)
REVERT: H  129 ASP cc_start: 0.7328 (p0) cc_final: 0.6836 (p0)
REVERT: H  130 MET cc_start: 0.6655 (mmm) cc_final: 0.6240 (mmm)
REVERT: I   13 MET cc_start: 0.8283 (mmm) cc_final: 0.7825 (mmm)
REVERT: I   93 MET cc_start: 0.7840 (mmt) cc_final: 0.7509 (mmt)
REVERT: I  183 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7313 (mt-10)
REVERT: I  196 PHE cc_start: 0.8455 (m-80) cc_final: 0.8037 (m-10)
  outliers start: 33
  outliers final: 18
  residues processed: 292
  average time/residue: 0.1245
  time to fit residues: 51.2891
Evaluate side-chains
  273 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 255
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain B residue    3 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain E residue   44 GLN
Chi-restraints excluded: chain E residue  130 MET
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 160 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 136 optimal weight:    1.9990
   chunk 154 optimal weight:    6.9990
   chunk 125 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 146 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
D 117 GLN
E  44 GLN
E  92 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.051405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.044331 restraints weight = 82571.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.045525 restraints weight = 48489.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.046350 restraints weight = 32434.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.046926 restraints weight = 23811.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.047330 restraints weight = 18719.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12546  Z= 0.150
  Angle     :  0.753  10.805  17019  Z= 0.388
  Chirality :  0.043   0.225   2143
  Planarity :  0.004   0.055   2174
  Dihedral  :  4.764  23.375   1773
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.07 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.20), residues: 1709
  helix:  1.17 (0.19), residues: 745
  sheet:  0.32 (0.37), residues: 203
  loop : -1.17 (0.22), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 100 
 TYR   0.012   0.001   TYR B 133 
 PHE   0.035   0.002   PHE C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (12537)
  covalent geometry    : angle       0.74720 (17001)
  SS BOND              : bond        0.00459 (    9)
  SS BOND              : angle       2.97035 (   18)
  hydrogen bonds       : bond        0.04040 (  714)
  hydrogen bonds       : angle       5.27314 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 267
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASP cc_start: 0.8601 (m-30) cc_final: 0.8240 (m-30)
REVERT: A  173 ASN cc_start: 0.8246 (t0) cc_final: 0.7946 (p0)
REVERT: B    1 MET cc_start: 0.8716 (tpp) cc_final: 0.8284 (tpp)
REVERT: B   83 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7990 (pm20)
REVERT: B  165 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7918 (ptmm)
REVERT: C   33 MET cc_start: 0.8752 (tmm) cc_final: 0.8490 (tmm)
REVERT: C   78 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7567 (tptp)
REVERT: D   33 MET cc_start: 0.7258 (mtt) cc_final: 0.6956 (mtt)
REVERT: D   94 ASN cc_start: 0.8885 (m-40) cc_final: 0.8675 (m110)
REVERT: D  129 ASP cc_start: 0.7416 (p0) cc_final: 0.7033 (p0)
REVERT: E   62 ASP cc_start: 0.8287 (p0) cc_final: 0.7968 (p0)
REVERT: E   93 MET cc_start: 0.6945 (mtt) cc_final: 0.6710 (mtt)
REVERT: E  196 PHE cc_start: 0.8054 (m-10) cc_final: 0.7703 (m-80)
REVERT: F   44 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: F   62 ASP cc_start: 0.8435 (p0) cc_final: 0.7935 (p0)
REVERT: F   93 MET cc_start: 0.8397 (mmm) cc_final: 0.8188 (tpt)
REVERT: G   38 GLN cc_start: 0.8683 (tp40) cc_final: 0.8343 (tp-100)
REVERT: G   49 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8474 (mm110)
REVERT: H   83 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7890 (tp30)
REVERT: I  183 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7321 (mt-10)
REVERT: I  196 PHE cc_start: 0.8463 (m-80) cc_final: 0.8024 (m-10)
  outliers start: 32
  outliers final: 21
  residues processed: 292
  average time/residue: 0.1230
  time to fit residues: 51.0555
Evaluate side-chains
  268 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 246
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   29 ASP
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain E residue   44 GLN
Chi-restraints excluded: chain E residue  130 MET
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  164 ILE
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 128 optimal weight:    0.0060
   chunk 5 optimal weight:    7.9990
   chunk 83 optimal weight:    0.0270
   chunk 158 optimal weight:    8.9990
   chunk 102 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 147 optimal weight:    5.9990
   overall best weight:    1.6060

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
B  92 ASN
D 117 GLN
E  44 GLN
G 198 ASN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.051957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.044742 restraints weight = 81653.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.045928 restraints weight = 48009.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.046745 restraints weight = 32068.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.047307 restraints weight = 23642.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.047674 restraints weight = 18783.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.5111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  12546  Z= 0.153
  Angle     :  0.805  16.735  17019  Z= 0.411
  Chirality :  0.043   0.219   2143
  Planarity :  0.004   0.049   2174
  Dihedral  :  4.824  30.175   1773
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 26.76 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.21), residues: 1709
  helix:  1.18 (0.19), residues: 751
  sheet:  0.33 (0.36), residues: 214
  loop : -1.08 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 100 
 TYR   0.011   0.001   TYR F 133 
 PHE   0.035   0.002   PHE C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (12537)
  covalent geometry    : angle       0.79154 (17001)
  SS BOND              : bond        0.00408 (    9)
  SS BOND              : angle       4.56420 (   18)
  hydrogen bonds       : bond        0.03973 (  714)
  hydrogen bonds       : angle       5.21977 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 255
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASP cc_start: 0.8626 (m-30) cc_final: 0.8355 (m-30)
REVERT: A  130 MET cc_start: 0.8896 (mpp) cc_final: 0.8471 (mpp)
REVERT: A  173 ASN cc_start: 0.8189 (t0) cc_final: 0.7907 (p0)
REVERT: B   33 MET cc_start: 0.8214 (mmm) cc_final: 0.7783 (mmm)
REVERT: B   83 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7980 (pm20)
REVERT: C   78 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7536 (tptp)
REVERT: E   62 ASP cc_start: 0.8313 (p0) cc_final: 0.8063 (p0)
REVERT: E   93 MET cc_start: 0.6940 (mtt) cc_final: 0.6740 (mtt)
REVERT: E  196 PHE cc_start: 0.8076 (m-10) cc_final: 0.7755 (m-80)
REVERT: F   44 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: F   62 ASP cc_start: 0.8461 (p0) cc_final: 0.7941 (p0)
REVERT: G   38 GLN cc_start: 0.8652 (tp40) cc_final: 0.8316 (tp-100)
REVERT: H   83 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7961 (tp30)
REVERT: H  100 ARG cc_start: 0.8305 (ptt90) cc_final: 0.7829 (ptp90)
REVERT: H  129 ASP cc_start: 0.7281 (p0) cc_final: 0.7007 (p0)
REVERT: I  183 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7288 (mt-10)
REVERT: I  196 PHE cc_start: 0.8439 (m-80) cc_final: 0.7996 (m-10)
  outliers start: 25
  outliers final: 18
  residues processed: 275
  average time/residue: 0.1198
  time to fit residues: 47.0462
Evaluate side-chains
  259 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 240
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain B residue    3 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain E residue   44 GLN
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   54 LEU
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 122 optimal weight:    1.9990
   chunk 144 optimal weight:    7.9990
   chunk 0 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 67 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 117 GLN
E  44 GLN
E 152 ASN
G 152 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.049304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.042269 restraints weight = 83008.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.043430 restraints weight = 48345.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.044212 restraints weight = 32189.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.044747 restraints weight = 23673.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.045089 restraints weight = 18825.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.5332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  12546  Z= 0.250
  Angle     :  0.880  17.152  17019  Z= 0.457
  Chirality :  0.045   0.210   2143
  Planarity :  0.004   0.046   2174
  Dihedral  :  5.371  32.976   1773
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 22.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 27.22 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.20), residues: 1709
  helix:  0.73 (0.19), residues: 750
  sheet:  0.12 (0.36), residues: 217
  loop : -1.15 (0.23), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 100 
 TYR   0.016   0.002   TYR G  57 
 PHE   0.039   0.003   PHE E 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (12537)
  covalent geometry    : angle       0.86658 (17001)
  SS BOND              : bond        0.00477 (    9)
  SS BOND              : angle       4.79760 (   18)
  hydrogen bonds       : bond        0.05025 (  714)
  hydrogen bonds       : angle       5.63564 ( 2043)

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

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

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3418 Ramachandran restraints generated.
    1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 254
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASP cc_start: 0.8726 (m-30) cc_final: 0.8378 (m-30)
REVERT: A  173 ASN cc_start: 0.8261 (t0) cc_final: 0.8017 (p0)
REVERT: B   83 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8165 (mp0)
REVERT: B  165 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7975 (pttp)
REVERT: C   78 LYS cc_start: 0.8153 (mmmm) cc_final: 0.7358 (tptp)
REVERT: D   33 MET cc_start: 0.7305 (mtt) cc_final: 0.6951 (mtp)
REVERT: E   62 ASP cc_start: 0.8512 (p0) cc_final: 0.8255 (p0)
REVERT: E  196 PHE cc_start: 0.8264 (m-10) cc_final: 0.8021 (m-10)
REVERT: F   44 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7864 (tm-30)
REVERT: F   62 ASP cc_start: 0.8453 (p0) cc_final: 0.7923 (p0)
REVERT: F   93 MET cc_start: 0.8411 (mmm) cc_final: 0.8150 (tpt)
REVERT: G    1 MET cc_start: 0.8084 (ppp) cc_final: 0.7847 (ppp)
REVERT: H   83 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7958 (tp30)
REVERT: H  100 ARG cc_start: 0.8345 (ptt90) cc_final: 0.8016 (ptp90)
REVERT: I   93 MET cc_start: 0.7609 (mmt) cc_final: 0.7385 (mmt)
REVERT: I  183 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7411 (mt-10)
REVERT: I  196 PHE cc_start: 0.8482 (m-80) cc_final: 0.8073 (m-10)
  outliers start: 33
  outliers final: 23
  residues processed: 277
  average time/residue: 0.1178
  time to fit residues: 46.8012
Evaluate side-chains
  274 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 250
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue  152 ASN
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain B residue    3 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain E residue   44 GLN
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  187 LYS
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   54 LEU
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  164 ILE
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 105 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 133 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 127 optimal weight:    5.9990
   chunk 144 optimal weight:    8.9990
   chunk 154 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 117 GLN
E  44 GLN
G  41 ASN
G 198 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.049008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.042060 restraints weight = 83470.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.043214 restraints weight = 48489.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.043995 restraints weight = 32263.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.044533 restraints weight = 23736.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.044895 restraints weight = 18853.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  12546  Z= 0.248
  Angle     :  0.885  18.040  17019  Z= 0.458
  Chirality :  0.045   0.228   2143
  Planarity :  0.004   0.049   2174
  Dihedral  :  5.601  33.583   1773
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 22.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 27.99 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.20), residues: 1709
  helix:  0.56 (0.18), residues: 757
  sheet:  0.07 (0.36), residues: 215
  loop : -1.25 (0.23), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 100 
 TYR   0.016   0.002   TYR G  57 
 PHE   0.042   0.003   PHE E 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (12537)
  covalent geometry    : angle       0.87467 (17001)
  SS BOND              : bond        0.00428 (    9)
  SS BOND              : angle       4.30186 (   18)
  hydrogen bonds       : bond        0.05041 (  714)
  hydrogen bonds       : angle       5.75092 ( 2043)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2081.56 seconds
wall clock time: 36 minutes 59.87 seconds (2219.87 seconds total)