Starting phenix.real_space_refine
on Wed Jul 30 09:24:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uhf_42279/07_2025/8uhf_42279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uhf_42279/07_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_42279/07_2025/8uhf_42279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uhf_42279/07_2025/8uhf_42279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uhf_42279/07_2025/8uhf_42279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uhf_42279/07_2025/8uhf_42279.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.121 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.01, per 1000 atoms: 0.65
  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.13
  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: 3.26

  Time building geometry restraints manager: 3.28 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:             0.690
  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:          0.490
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     28.680
  Find NCS groups from input model:        0.810
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.420
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (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
 PHE   0.008   0.001   PHE G 108 
 TYR   0.004   0.001   TYR G 133 
 ARG   0.002   0.000   ARG E  52 

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

*********************** 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  : 1.358 
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: 0.3155
  time to fit residues: 173.1651
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  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    1.9990
   chunk 128 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 68 optimal weight:    8.9990
   chunk 133 optimal weight:    0.0470
   chunk 51 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 99 optimal weight:    0.8980
   chunk 154 optimal weight:   10.0000
   overall best weight:    2.3884

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.051991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.044927 restraints weight = 80348.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.046166 restraints weight = 47194.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.047015 restraints weight = 31363.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12546  Z= 0.148
  Angle     :  0.655  11.763  17019  Z= 0.343
  Chirality :  0.042   0.160   2143
  Planarity :  0.004   0.035   2174
  Dihedral  :  4.417  19.742   1773
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.87 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.20), residues: 1709
  helix:  0.81 (0.19), residues: 753
  sheet: -0.53 (0.32), residues: 222
  loop : -1.67 (0.21), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.026   0.002   PHE E 196 
 TYR   0.016   0.002   TYR C 133 
 ARG   0.005   0.001   ARG F 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  714)
  hydrogen bonds       : angle       5.38068 ( 2043)
  SS BOND              : bond        0.00673 (    9)
  SS BOND              : angle       1.80845 (   18)
  covalent geometry    : bond        0.00319 (12537)
  covalent geometry    : angle       0.65228 (17001)

*********************** 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
  357 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 341
  time to evaluate  : 1.246 
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   93 MET cc_start: 0.6647 (mtt) cc_final: 0.6389 (mtt)
REVERT: A  137 LYS cc_start: 0.9290 (tptt) cc_final: 0.8941 (mppt)
REVERT: A  173 ASN cc_start: 0.8563 (t0) cc_final: 0.8132 (p0)
REVERT: B   33 MET cc_start: 0.8570 (mmm) cc_final: 0.8238 (mmm)
REVERT: B   94 ASN cc_start: 0.8272 (t0) cc_final: 0.7330 (t0)
REVERT: B   96 PHE cc_start: 0.7588 (m-80) cc_final: 0.6651 (m-10)
REVERT: B  133 TYR cc_start: 0.7926 (t80) cc_final: 0.7568 (t80)
REVERT: C   33 MET cc_start: 0.8696 (tmm) cc_final: 0.8391 (tmm)
REVERT: C   78 LYS cc_start: 0.8356 (mmmm) cc_final: 0.7785 (mmmt)
REVERT: C  129 ASP cc_start: 0.8889 (p0) cc_final: 0.8638 (p0)
REVERT: C  131 PHE cc_start: 0.6736 (m-80) cc_final: 0.6535 (m-80)
REVERT: C  192 PHE cc_start: 0.6486 (m-80) cc_final: 0.6258 (m-10)
REVERT: D   13 MET cc_start: 0.8770 (mmm) cc_final: 0.8467 (mmm)
REVERT: D  129 ASP cc_start: 0.7300 (p0) cc_final: 0.6963 (p0)
REVERT: D  174 LEU cc_start: 0.9061 (mp) cc_final: 0.8773 (mp)
REVERT: E   25 GLN cc_start: 0.7734 (mt0) cc_final: 0.7352 (mt0)
REVERT: E   83 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8379 (tp30)
REVERT: F   44 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7693 (tm-30)
REVERT: F   62 ASP cc_start: 0.8514 (p0) cc_final: 0.8012 (p0)
REVERT: G   38 GLN cc_start: 0.8685 (tp40) cc_final: 0.8438 (tp-100)
REVERT: G   49 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8623 (mm110)
REVERT: H   98 PHE cc_start: 0.7507 (p90) cc_final: 0.7171 (p90)
REVERT: I  183 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7198 (mt-10)
REVERT: I  196 PHE cc_start: 0.8415 (m-80) cc_final: 0.7949 (m-10)
  outliers start: 16
  outliers final: 8
  residues processed: 347
  average time/residue: 0.2887
  time to fit residues: 136.0524
Evaluate side-chains
  280 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 272
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9980
   chunk 105 optimal weight:    8.9990
   chunk 158 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 123 optimal weight:   20.0000
   chunk 86 optimal weight:   10.0000
   chunk 160 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 55 optimal weight:    1.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 119 GLN
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 GLN
E 105 ASN
F  41 ASN
G 101 ASN
G 152 ASN
G 198 ASN
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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.049370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.042375 restraints weight = 82644.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.043561 restraints weight = 48147.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.044372 restraints weight = 31921.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12546  Z= 0.215
  Angle     :  0.708  11.558  17019  Z= 0.373
  Chirality :  0.043   0.157   2143
  Planarity :  0.004   0.041   2174
  Dihedral  :  4.939  21.427   1773
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.94 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.20), residues: 1709
  helix:  0.83 (0.19), residues: 754
  sheet: -0.30 (0.33), residues: 221
  loop : -1.40 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.034   0.002   PHE E 196 
 TYR   0.015   0.002   TYR F 133 
 ARG   0.010   0.001   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04724 (  714)
  hydrogen bonds       : angle       5.57563 ( 2043)
  SS BOND              : bond        0.00649 (    9)
  SS BOND              : angle       2.68062 (   18)
  covalent geometry    : bond        0.00454 (12537)
  covalent geometry    : angle       0.70251 (17001)

*********************** 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
  327 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 297
  time to evaluate  : 1.437 
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: A   41 ASN cc_start: 0.8463 (m-40) cc_final: 0.8225 (p0)
REVERT: A   93 MET cc_start: 0.6682 (mtt) cc_final: 0.6444 (mtt)
REVERT: A  137 LYS cc_start: 0.9187 (tptt) cc_final: 0.8912 (mppt)
REVERT: A  173 ASN cc_start: 0.8433 (t0) cc_final: 0.8075 (p0)
REVERT: B   83 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7955 (mp0)
REVERT: B   94 ASN cc_start: 0.8237 (t0) cc_final: 0.7173 (t0)
REVERT: B   96 PHE cc_start: 0.7543 (m-80) cc_final: 0.6523 (m-10)
REVERT: C  110 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7726 (mp)
REVERT: C  129 ASP cc_start: 0.8876 (p0) cc_final: 0.8618 (p0)
REVERT: E   62 ASP cc_start: 0.8493 (p0) cc_final: 0.8279 (p0)
REVERT: E   68 LYS cc_start: 0.9079 (mttp) cc_final: 0.8754 (mmtp)
REVERT: F   44 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7746 (tm-30)
REVERT: F   62 ASP cc_start: 0.8532 (p0) cc_final: 0.8094 (p0)
REVERT: G   38 GLN cc_start: 0.8736 (tp40) cc_final: 0.8485 (tp-100)
REVERT: H   83 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8022 (tp30)
REVERT: H   98 PHE cc_start: 0.7466 (p90) cc_final: 0.7082 (p90)
REVERT: H  174 LEU cc_start: 0.9264 (tt) cc_final: 0.8615 (mp)
REVERT: I   13 MET cc_start: 0.8075 (mmm) cc_final: 0.7839 (mtt)
REVERT: I  183 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7298 (mt-10)
REVERT: I  196 PHE cc_start: 0.8462 (m-80) cc_final: 0.8075 (m-10)
  outliers start: 30
  outliers final: 13
  residues processed: 312
  average time/residue: 0.2651
  time to fit residues: 115.6912
Evaluate side-chains
  275 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 261
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
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   56 ASN
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain C residue  110 ILE
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain E residue  187 LYS
Chi-restraints excluded: chain F residue  123 LEU
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 130 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 146 optimal weight:    1.9990
   chunk 166 optimal weight:   20.0000
   chunk 5 optimal weight:   20.0000
   chunk 141 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 134 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 105 ASN
A 119 GLN
B  25 GLN
D  94 ASN
G  56 ASN
** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.049580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.042537 restraints weight = 81354.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.043713 restraints weight = 47744.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.044527 restraints weight = 31719.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12546  Z= 0.178
  Angle     :  0.675  11.674  17019  Z= 0.355
  Chirality :  0.042   0.153   2143
  Planarity :  0.004   0.037   2174
  Dihedral  :  4.925  23.170   1773
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.09 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.20), residues: 1709
  helix:  0.92 (0.19), residues: 752
  sheet: -0.18 (0.34), residues: 218
  loop : -1.22 (0.23), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.021   0.002   PHE C 131 
 TYR   0.016   0.002   TYR E 133 
 ARG   0.006   0.001   ARG H 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04471 (  714)
  hydrogen bonds       : angle       5.48716 ( 2043)
  SS BOND              : bond        0.00457 (    9)
  SS BOND              : angle       1.84892 (   18)
  covalent geometry    : bond        0.00378 (12537)
  covalent geometry    : angle       0.67262 (17001)

*********************** 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
  315 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 283
  time to evaluate  : 1.533 
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   68 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7849 (tptt)
REVERT: A  137 LYS cc_start: 0.9240 (tptt) cc_final: 0.8919 (mppt)
REVERT: A  173 ASN cc_start: 0.8479 (t0) cc_final: 0.8049 (p0)
REVERT: B   94 ASN cc_start: 0.8268 (t0) cc_final: 0.7463 (t0)
REVERT: B   96 PHE cc_start: 0.7616 (m-80) cc_final: 0.6659 (m-10)
REVERT: C  129 ASP cc_start: 0.8949 (p0) cc_final: 0.8656 (p0)
REVERT: C  192 PHE cc_start: 0.7290 (m-80) cc_final: 0.6895 (m-10)
REVERT: D   10 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (tp)
REVERT: E   62 ASP cc_start: 0.8503 (p0) cc_final: 0.8263 (p0)
REVERT: F   44 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: F   62 ASP cc_start: 0.8513 (p0) cc_final: 0.8004 (p0)
REVERT: G    1 MET cc_start: 0.7070 (ttm) cc_final: 0.6691 (ttp)
REVERT: G   38 GLN cc_start: 0.8758 (tp40) cc_final: 0.8488 (tp-100)
REVERT: G   52 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8567 (mmm160)
REVERT: H   83 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8033 (tp30)
REVERT: H   98 PHE cc_start: 0.7569 (p90) cc_final: 0.7179 (p90)
REVERT: H  174 LEU cc_start: 0.9231 (tt) cc_final: 0.8596 (mp)
REVERT: I  183 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7306 (mt-10)
REVERT: I  196 PHE cc_start: 0.8458 (m-80) cc_final: 0.8012 (m-10)
  outliers start: 32
  outliers final: 14
  residues processed: 308
  average time/residue: 0.2708
  time to fit residues: 115.8456
Evaluate side-chains
  264 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 249
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   82 ASP
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 E residue    2 THR
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  187 LYS
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue   91 THR
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 113 optimal weight:    6.9990
   chunk 163 optimal weight:    9.9990
   chunk 131 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0000
   chunk 169 optimal weight:    6.9990
   chunk 166 optimal weight:    7.9990
   chunk 103 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    3.7992

-------------------------------------------------------------------------------
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
E  44 GLN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.049458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.042448 restraints weight = 81390.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.043635 restraints weight = 47544.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.044445 restraints weight = 31506.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12546  Z= 0.179
  Angle     :  0.691   9.627  17019  Z= 0.364
  Chirality :  0.042   0.157   2143
  Planarity :  0.004   0.043   2174
  Dihedral  :  4.988  23.767   1773
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.78 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.20), residues: 1709
  helix:  0.95 (0.19), residues: 748
  sheet: -0.06 (0.35), residues: 217
  loop : -1.19 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.029   0.002   PHE E 196 
 TYR   0.011   0.002   TYR B 133 
 ARG   0.009   0.001   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04485 (  714)
  hydrogen bonds       : angle       5.44613 ( 2043)
  SS BOND              : bond        0.00293 (    9)
  SS BOND              : angle       1.93833 (   18)
  covalent geometry    : bond        0.00385 (12537)
  covalent geometry    : angle       0.68865 (17001)

*********************** 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
  307 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 269
  time to evaluate  : 1.256 
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   68 LYS cc_start: 0.8040 (tmtt) cc_final: 0.7809 (tptt)
REVERT: A   82 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8490 (p0)
REVERT: A   83 GLU cc_start: 0.7819 (pt0) cc_final: 0.7325 (pt0)
REVERT: A  137 LYS cc_start: 0.9239 (tptt) cc_final: 0.8962 (mppt)
REVERT: B   96 PHE cc_start: 0.7700 (m-80) cc_final: 0.7247 (m-10)
REVERT: C   33 MET cc_start: 0.8614 (tmm) cc_final: 0.8223 (tmm)
REVERT: C  129 ASP cc_start: 0.8910 (p0) cc_final: 0.8594 (p0)
REVERT: C  151 GLU cc_start: 0.7879 (mp0) cc_final: 0.7439 (mp0)
REVERT: C  192 PHE cc_start: 0.7404 (m-80) cc_final: 0.7130 (m-10)
REVERT: D   10 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7872 (tp)
REVERT: D   94 ASN cc_start: 0.8964 (m-40) cc_final: 0.8655 (m110)
REVERT: E   62 ASP cc_start: 0.8447 (p0) cc_final: 0.8192 (p0)
REVERT: F   44 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7720 (tm-30)
REVERT: F   62 ASP cc_start: 0.8505 (p0) cc_final: 0.8000 (p0)
REVERT: G   13 MET cc_start: 0.8920 (mmm) cc_final: 0.8656 (mmm)
REVERT: G   38 GLN cc_start: 0.8746 (tp40) cc_final: 0.8485 (tp-100)
REVERT: G   96 PHE cc_start: 0.7023 (m-80) cc_final: 0.6792 (m-10)
REVERT: G  117 GLN cc_start: 0.8945 (mp10) cc_final: 0.8677 (mp10)
REVERT: H   83 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7998 (tp30)
REVERT: H   98 PHE cc_start: 0.7624 (p90) cc_final: 0.7129 (p90)
REVERT: H  174 LEU cc_start: 0.9225 (tt) cc_final: 0.8610 (mp)
REVERT: I  183 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7303 (mt-10)
REVERT: I  196 PHE cc_start: 0.8457 (m-80) cc_final: 0.8034 (m-10)
  outliers start: 38
  outliers final: 22
  residues processed: 300
  average time/residue: 0.2723
  time to fit residues: 115.1540
Evaluate side-chains
  275 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 251
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain A residue   82 ASP
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain E residue  187 LYS
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 H residue   91 THR
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  108 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 159 optimal weight:    9.9990
   chunk 91 optimal weight:    0.4980
   chunk 102 optimal weight:    6.9990
   chunk 155 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 169 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 110 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    3.0986

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.050098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.042950 restraints weight = 82952.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.044121 restraints weight = 49037.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.044928 restraints weight = 32735.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12546  Z= 0.162
  Angle     :  0.696   8.999  17019  Z= 0.362
  Chirality :  0.042   0.176   2143
  Planarity :  0.004   0.048   2174
  Dihedral  :  4.959  23.486   1773
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.93 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.20), residues: 1709
  helix:  1.04 (0.19), residues: 753
  sheet: -0.02 (0.35), residues: 218
  loop : -1.17 (0.23), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.032   0.002   PHE E 196 
 TYR   0.009   0.001   TYR H 133 
 ARG   0.008   0.001   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04298 (  714)
  hydrogen bonds       : angle       5.39670 ( 2043)
  SS BOND              : bond        0.00391 (    9)
  SS BOND              : angle       1.66787 (   18)
  covalent geometry    : bond        0.00351 (12537)
  covalent geometry    : angle       0.69396 (17001)

*********************** 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: 35
    poor density    : 272
  time to evaluate  : 1.356 
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: A   44 GLN cc_start: 0.9199 (pp30) cc_final: 0.8901 (pp30)
REVERT: A   83 GLU cc_start: 0.7883 (pt0) cc_final: 0.7584 (pt0)
REVERT: B   96 PHE cc_start: 0.7812 (m-80) cc_final: 0.7337 (m-10)
REVERT: C   33 MET cc_start: 0.8654 (tmm) cc_final: 0.8267 (tmm)
REVERT: C  131 PHE cc_start: 0.6983 (m-10) cc_final: 0.6182 (m-10)
REVERT: C  192 PHE cc_start: 0.7393 (m-80) cc_final: 0.7168 (m-10)
REVERT: D   10 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7817 (tp)
REVERT: D   92 ASN cc_start: 0.8923 (t0) cc_final: 0.8702 (t0)
REVERT: D   94 ASN cc_start: 0.8971 (m-40) cc_final: 0.8664 (m110)
REVERT: D  173 ASN cc_start: 0.8554 (m110) cc_final: 0.8252 (t0)
REVERT: E   62 ASP cc_start: 0.8485 (p0) cc_final: 0.8231 (p0)
REVERT: E   83 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8490 (tp30)
REVERT: F   44 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7662 (tm-30)
REVERT: F   62 ASP cc_start: 0.8442 (p0) cc_final: 0.7922 (p0)
REVERT: G   38 GLN cc_start: 0.8746 (tp40) cc_final: 0.8449 (tp-100)
REVERT: G   96 PHE cc_start: 0.7036 (m-80) cc_final: 0.6752 (m-10)
REVERT: G  117 GLN cc_start: 0.8969 (mp10) cc_final: 0.8716 (mp10)
REVERT: G  198 ASN cc_start: 0.6310 (m-40) cc_final: 0.5552 (m-40)
REVERT: H   32 ASN cc_start: 0.8931 (m-40) cc_final: 0.8695 (m110)
REVERT: H   83 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7875 (tp30)
REVERT: H   98 PHE cc_start: 0.7623 (p90) cc_final: 0.7153 (p90)
REVERT: H  174 LEU cc_start: 0.9192 (tt) cc_final: 0.8494 (mp)
REVERT: I  183 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7331 (mt-10)
REVERT: I  196 PHE cc_start: 0.8434 (m-80) cc_final: 0.7991 (m-10)
  outliers start: 35
  outliers final: 23
  residues processed: 299
  average time/residue: 0.2480
  time to fit residues: 104.4138
Evaluate side-chains
  277 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 252
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain E residue  187 LYS
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  173 ASN
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue   93 MET
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 109 optimal weight:    3.9990
   chunk 150 optimal weight:   30.0000
   chunk 81 optimal weight:    4.9990
   chunk 96 optimal weight:    9.9990
   chunk 114 optimal weight:    1.9990
   chunk 33 optimal weight:   30.0000
   chunk 87 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0270
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.6044

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

Flipped N/Q/H residues before XYZ refinement:
B  25 GLN
E  44 GLN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.051284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.043994 restraints weight = 82732.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.045174 restraints weight = 48458.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.045985 restraints weight = 32459.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4681

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= 0.139
  Angle     :  0.699  10.251  17019  Z= 0.362
  Chirality :  0.042   0.216   2143
  Planarity :  0.004   0.050   2174
  Dihedral  :  4.779  23.268   1773
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 26.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.20), residues: 1709
  helix:  1.22 (0.19), residues: 752
  sheet:  0.18 (0.36), residues: 207
  loop : -1.19 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.025   0.002   PHE F 150 
 TYR   0.024   0.002   TYR F 133 
 ARG   0.012   0.001   ARG A 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  714)
  hydrogen bonds       : angle       5.21539 ( 2043)
  SS BOND              : bond        0.00550 (    9)
  SS BOND              : angle       1.75414 (   18)
  covalent geometry    : bond        0.00308 (12537)
  covalent geometry    : angle       0.69712 (17001)

*********************** 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
  312 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 282
  time to evaluate  : 1.519 
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: symmetry clash
REVERT: A   68 LYS cc_start: 0.8088 (tmtt) cc_final: 0.7888 (tptt)
REVERT: A   83 GLU cc_start: 0.7855 (pt0) cc_final: 0.7598 (pt0)
REVERT: A  129 ASP cc_start: 0.8580 (m-30) cc_final: 0.8203 (m-30)
REVERT: A  173 ASN cc_start: 0.8482 (t0) cc_final: 0.8004 (p0)
REVERT: B   96 PHE cc_start: 0.7827 (m-80) cc_final: 0.7548 (m-80)
REVERT: D   10 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7692 (tp)
REVERT: D   94 ASN cc_start: 0.8903 (m-40) cc_final: 0.8658 (m110)
REVERT: D  129 ASP cc_start: 0.7449 (p0) cc_final: 0.7064 (p0)
REVERT: D  173 ASN cc_start: 0.8446 (m110) cc_final: 0.8193 (t0)
REVERT: E   62 ASP cc_start: 0.8523 (p0) cc_final: 0.8180 (p0)
REVERT: F   44 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7717 (tm-30)
REVERT: F   62 ASP cc_start: 0.8476 (p0) cc_final: 0.7954 (p0)
REVERT: F   88 PHE cc_start: 0.7877 (m-80) cc_final: 0.7673 (m-80)
REVERT: G   38 GLN cc_start: 0.8731 (tp40) cc_final: 0.8416 (tp-100)
REVERT: H   32 ASN cc_start: 0.8949 (m-40) cc_final: 0.8737 (m110)
REVERT: H   83 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7915 (tp30)
REVERT: H  174 LEU cc_start: 0.8960 (tt) cc_final: 0.8341 (mp)
REVERT: I  183 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7345 (mt-10)
REVERT: I  196 PHE cc_start: 0.8421 (m-80) cc_final: 0.7974 (m-10)
  outliers start: 30
  outliers final: 20
  residues processed: 303
  average time/residue: 0.2685
  time to fit residues: 114.3982
Evaluate side-chains
  269 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 248
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   44 GLN
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain E residue  187 LYS
Chi-restraints excluded: chain F residue  112 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 H residue   81 SER
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue   93 MET
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 120 optimal weight:    5.9990
   chunk 164 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9990
   chunk 161 optimal weight:    0.6980
   chunk 90 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 168 optimal weight:    9.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
E  44 GLN
G  41 ASN
G 198 ASN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 101 ASN
** 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 = 0.3339 r_free = 0.3339 target = 0.050909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.043721 restraints weight = 83196.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.044913 restraints weight = 48783.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.045729 restraints weight = 32439.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4906

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= 0.157
  Angle     :  0.737  10.516  17019  Z= 0.379
  Chirality :  0.043   0.201   2143
  Planarity :  0.004   0.049   2174
  Dihedral  :  4.853  24.808   1773
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.61 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.20), residues: 1709
  helix:  1.10 (0.19), residues: 749
  sheet:  0.22 (0.37), residues: 208
  loop : -1.18 (0.22), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.027   0.002   PHE C 196 
 TYR   0.023   0.002   TYR F 133 
 ARG   0.014   0.001   ARG H 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04126 (  714)
  hydrogen bonds       : angle       5.30018 ( 2043)
  SS BOND              : bond        0.00366 (    9)
  SS BOND              : angle       1.70796 (   18)
  covalent geometry    : bond        0.00347 (12537)
  covalent geometry    : angle       0.73552 (17001)

*********************** 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
  289 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 258
  time to evaluate  : 1.395 
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: 0.8112 (tmtt) cc_final: 0.7890 (tptt)
REVERT: A   83 GLU cc_start: 0.7963 (pt0) cc_final: 0.7748 (pt0)
REVERT: A  129 ASP cc_start: 0.8664 (m-30) cc_final: 0.8307 (m-30)
REVERT: A  173 ASN cc_start: 0.8480 (t0) cc_final: 0.8012 (p0)
REVERT: B   82 ASP cc_start: 0.8456 (p0) cc_final: 0.8112 (p0)
REVERT: B   96 PHE cc_start: 0.7942 (m-80) cc_final: 0.7628 (m-80)
REVERT: D   10 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7777 (tp)
REVERT: D   94 ASN cc_start: 0.8968 (m-40) cc_final: 0.8659 (m110)
REVERT: D  129 ASP cc_start: 0.7546 (p0) cc_final: 0.7185 (p0)
REVERT: E    2 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8053 (m)
REVERT: E   62 ASP cc_start: 0.8537 (p0) cc_final: 0.8263 (p0)
REVERT: E   93 MET cc_start: 0.6989 (mtt) cc_final: 0.6766 (mtt)
REVERT: E  196 PHE cc_start: 0.8037 (m-10) cc_final: 0.7528 (m-80)
REVERT: F   44 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7840 (tm-30)
REVERT: F   62 ASP cc_start: 0.8549 (p0) cc_final: 0.8031 (p0)
REVERT: F   93 MET cc_start: 0.8838 (mmm) cc_final: 0.8168 (mmm)
REVERT: F   94 ASN cc_start: 0.8908 (m110) cc_final: 0.8653 (m-40)
REVERT: G   38 GLN cc_start: 0.8796 (tp40) cc_final: 0.8485 (tp-100)
REVERT: G  198 ASN cc_start: 0.5842 (m-40) cc_final: 0.5565 (m-40)
REVERT: H   83 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8028 (tp30)
REVERT: H  100 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7712 (ttm110)
REVERT: H  174 LEU cc_start: 0.9034 (tt) cc_final: 0.8380 (mp)
REVERT: I  183 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7353 (mt-10)
REVERT: I  196 PHE cc_start: 0.8481 (m-80) cc_final: 0.8043 (m-10)
  outliers start: 31
  outliers final: 20
  residues processed: 281
  average time/residue: 0.2535
  time to fit residues: 101.1567
Evaluate side-chains
  264 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 242
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   40 LEU
Chi-restraints excluded: chain D residue    8 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   44 GLN
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain F residue  112 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 H residue   81 SER
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue   73 LEU
Chi-restraints excluded: chain I residue   93 MET
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 126 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 96 optimal weight:    8.9990
   chunk 124 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 64 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 141 optimal weight:    0.5980
   chunk 151 optimal weight:    6.9990
   chunk 132 optimal weight:    5.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
B  25 GLN
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 117 GLN
** E  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 152 ASN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  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 = 0.3300 r_free = 0.3300 target = 0.049804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.042759 restraints weight = 82402.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.043912 restraints weight = 47918.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.044689 restraints weight = 31972.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.5097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12546  Z= 0.196
  Angle     :  0.791  13.771  17019  Z= 0.406
  Chirality :  0.044   0.210   2143
  Planarity :  0.004   0.048   2174
  Dihedral  :  5.078  25.725   1773
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 19.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 28.07 %
    Favored  : 69.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.20), residues: 1709
  helix:  0.87 (0.19), residues: 753
  sheet:  0.24 (0.37), residues: 206
  loop : -1.21 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.031   0.002   PHE H 131 
 TYR   0.026   0.002   TYR F 133 
 ARG   0.010   0.001   ARG H 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04586 (  714)
  hydrogen bonds       : angle       5.49101 ( 2043)
  SS BOND              : bond        0.00520 (    9)
  SS BOND              : angle       1.80683 (   18)
  covalent geometry    : bond        0.00426 (12537)
  covalent geometry    : angle       0.78925 (17001)

*********************** 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
  282 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 255
  time to evaluate  : 1.608 
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: A   68 LYS cc_start: 0.8095 (tmtt) cc_final: 0.7862 (tptt)
REVERT: A   83 GLU cc_start: 0.7926 (pt0) cc_final: 0.7580 (pt0)
REVERT: B   33 MET cc_start: 0.8227 (mmm) cc_final: 0.7776 (mmm)
REVERT: B   82 ASP cc_start: 0.8456 (p0) cc_final: 0.8214 (p0)
REVERT: C  196 PHE cc_start: 0.7765 (m-80) cc_final: 0.7317 (t80)
REVERT: D   10 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7858 (tp)
REVERT: E   62 ASP cc_start: 0.8613 (p0) cc_final: 0.8204 (p0)
REVERT: E   83 GLU cc_start: 0.8662 (tp30) cc_final: 0.8186 (tp30)
REVERT: E   93 MET cc_start: 0.6991 (mtt) cc_final: 0.6755 (mtt)
REVERT: E  196 PHE cc_start: 0.8097 (m-10) cc_final: 0.7744 (m-80)
REVERT: F   44 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: F   62 ASP cc_start: 0.8439 (p0) cc_final: 0.7967 (p0)
REVERT: F   93 MET cc_start: 0.8772 (mmm) cc_final: 0.8201 (mmm)
REVERT: F   94 ASN cc_start: 0.8818 (m110) cc_final: 0.8609 (m-40)
REVERT: G   38 GLN cc_start: 0.8701 (tp40) cc_final: 0.8450 (tp-100)
REVERT: G   62 ASP cc_start: 0.8059 (p0) cc_final: 0.7848 (p0)
REVERT: G   96 PHE cc_start: 0.7022 (m-80) cc_final: 0.6757 (m-10)
REVERT: H   83 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8007 (tp30)
REVERT: H  174 LEU cc_start: 0.9006 (tt) cc_final: 0.8361 (mp)
REVERT: I  183 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: I  196 PHE cc_start: 0.8458 (m-80) cc_final: 0.8051 (m-10)
  outliers start: 27
  outliers final: 21
  residues processed: 275
  average time/residue: 0.3301
  time to fit residues: 130.1498
Evaluate side-chains
  267 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 245
  time to evaluate  : 3.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  176 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   10 LEU
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   82 ASP
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue   93 MET
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 127 optimal weight:    8.9990
   chunk 115 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 26 optimal weight:    2.9990
   chunk 164 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 139 optimal weight:    4.9990
   chunk 163 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0670
   chunk 48 optimal weight:    6.9990
   overall best weight:    4.2126

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 ASN
D 117 GLN
E  44 GLN
** E  92 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**
** H 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 = 0.3296 r_free = 0.3296 target = 0.049658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.042570 restraints weight = 83302.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.043728 restraints weight = 48201.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.044521 restraints weight = 32018.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.5244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12546  Z= 0.200
  Angle     :  0.806  10.066  17019  Z= 0.413
  Chirality :  0.044   0.208   2143
  Planarity :  0.004   0.050   2174
  Dihedral  :  5.219  30.454   1773
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 20.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 28.22 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.20), residues: 1709
  helix:  0.81 (0.19), residues: 752
  sheet:  0.13 (0.37), residues: 206
  loop : -1.34 (0.23), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.030   0.002   PHE H 131 
 TYR   0.028   0.002   TYR F 133 
 ARG   0.011   0.001   ARG H 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04639 (  714)
  hydrogen bonds       : angle       5.61479 ( 2043)
  SS BOND              : bond        0.00395 (    9)
  SS BOND              : angle       1.70531 (   18)
  covalent geometry    : bond        0.00437 (12537)
  covalent geometry    : angle       0.80406 (17001)

********************** 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
  285 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 252
  time to evaluate  : 2.661 
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   68 LYS cc_start: 0.8092 (tmtt) cc_final: 0.7856 (tptt)
REVERT: B   82 ASP cc_start: 0.8412 (p0) cc_final: 0.8181 (p0)
REVERT: C  196 PHE cc_start: 0.7791 (m-80) cc_final: 0.7244 (t80)
REVERT: D   10 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7861 (tp)
REVERT: D  173 ASN cc_start: 0.8523 (m-40) cc_final: 0.8091 (m-40)
REVERT: E    2 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8323 (m)
REVERT: E   62 ASP cc_start: 0.8566 (p0) cc_final: 0.8235 (p0)
REVERT: E   93 MET cc_start: 0.6991 (mtt) cc_final: 0.6778 (mtt)
REVERT: E  196 PHE cc_start: 0.8118 (m-10) cc_final: 0.7756 (m-80)
REVERT: F   44 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7943 (tm-30)
REVERT: F   62 ASP cc_start: 0.8493 (p0) cc_final: 0.7951 (p0)
REVERT: F   93 MET cc_start: 0.8775 (mmm) cc_final: 0.8186 (mmm)
REVERT: F   94 ASN cc_start: 0.8787 (m110) cc_final: 0.8556 (m-40)
REVERT: G   38 GLN cc_start: 0.8719 (tp40) cc_final: 0.8474 (tp-100)
REVERT: H   83 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8008 (tp30)
REVERT: H  174 LEU cc_start: 0.9048 (tt) cc_final: 0.8395 (mp)
REVERT: I  183 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7362 (mt-10)
REVERT: I  196 PHE cc_start: 0.8477 (m-80) cc_final: 0.8065 (m-10)
  outliers start: 33
  outliers final: 24
  residues processed: 278
  average time/residue: 0.3907
  time to fit residues: 154.2722
Evaluate side-chains
  266 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 240
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  176 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   10 LEU
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue   94 ASN
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue   44 GLN
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  186 CYS
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain G residue   54 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   82 ASP
Chi-restraints excluded: chain G residue  176 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain I residue    6 VAL
Chi-restraints excluded: chain I residue   93 MET
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 61 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 85 optimal weight:    0.2980
   chunk 91 optimal weight:    7.9990
   chunk 148 optimal weight:    0.2980
   chunk 130 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
D  94 ASN
D 117 GLN
E  44 GLN
** E  92 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**
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  49 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.050838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.043670 restraints weight = 81990.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.044868 restraints weight = 47811.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.045681 restraints weight = 31700.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.5268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12546  Z= 0.154
  Angle     :  0.784  12.992  17019  Z= 0.397
  Chirality :  0.043   0.203   2143
  Planarity :  0.004   0.077   2174
  Dihedral  :  5.024  30.025   1773
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 28.14 %
    Favored  : 69.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.20), residues: 1709
  helix:  0.96 (0.19), residues: 748
  sheet:  0.06 (0.37), residues: 204
  loop : -1.32 (0.22), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.037   0.002   PHE H 131 
 TYR   0.026   0.002   TYR F 133 
 ARG   0.010   0.001   ARG H 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  714)
  hydrogen bonds       : angle       5.43708 ( 2043)
  SS BOND              : bond        0.00383 (    9)
  SS BOND              : angle       2.93171 (   18)
  covalent geometry    : bond        0.00346 (12537)
  covalent geometry    : angle       0.77810 (17001)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4640.23 seconds
wall clock time: 84 minutes 0.27 seconds (5040.27 seconds total)