Starting phenix.real_space_refine
on Wed Sep 17 07:14:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vuz_43545/09_2025/8vuz_43545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vuz_43545/09_2025/8vuz_43545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vuz_43545/09_2025/8vuz_43545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vuz_43545/09_2025/8vuz_43545.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vuz_43545/09_2025/8vuz_43545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vuz_43545/09_2025/8vuz_43545.map"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
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      23      5.16       5
     C    4166      2.51       5
     N    1114      2.21       5
     O    1323      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6626
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1652
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204}
    Chain: "B"
      Number of atoms: 1696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1696
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207}
    Chain: "H"
      Number of atoms: 1688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1688
          Classifications: {'peptide': 223}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1590
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197}
  Time building chain proxies: 1.63, per 1000 atoms: 0.25
  Number of scatterers: 6626
  At special positions: 0
  Unit cell: (59.76, 67.23, 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      23     16.00
     O    1323      8.00
     N    1114      7.00
     C    4166      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 141 " - pdb=" SG  CYS H 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 353.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1622

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 20 sheets defined
      7.0% alpha, 41.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 64
      removed outlier: 3.629A  pdb=" N   GLU A  64 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 61 through 64'
    Processing helix  chain 'A' and resid 83 through 87
      removed outlier: 3.762A  pdb=" N   SER A  87 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.868A  pdb=" N   LEU B  83 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 3.778A  pdb=" N   THR B 126 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 189
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.663A  pdb=" N   LYS H  64 " --> pdb=" O   GLU H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 98 through 100B
      removed outlier: 3.639A  pdb=" N   GLY H 100A" --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 188 through 193
      removed outlier: 3.954A  pdb=" N   THR H 192 " --> pdb=" O   SER H 188 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.911A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 128
    Processing helix  chain 'L' and resid 183 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.616A  pdb=" N   VAL A  18 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.282A  pdb=" N   GLU A  10 " --> pdb=" O   THR A 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 124
      removed outlier: 3.536A  pdb=" N   GLY A 139 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY A 144 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TYR A 175 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 124
      removed outlier: 3.536A  pdb=" N   GLY A 139 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY A 144 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TYR A 175 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 154
      removed outlier: 7.007A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 210 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   CYS A 195 " --> pdb=" O   LYS A 208 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.741A  pdb=" N   THR B   5 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ARG B  24 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.606A  pdb=" N   GLY B  84 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU B  37 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118
      removed outlier: 3.990A  pdb=" N   VAL B 133 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   CYS B 134 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118
      removed outlier: 3.990A  pdb=" N   VAL B 133 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   PHE B 139 " --> pdb=" O   TYR B 173 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154
      removed outlier: 3.720A  pdb=" N   ASN B 145 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B 193 " --> pdb=" O   LYS B 149 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.705A  pdb=" N   TRP H  35A" --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ARG H  50 " --> pdb=" O   TRP H  35A" (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 120 through 123
      removed outlier: 5.968A  pdb=" N   TYR H 177 " --> pdb=" O   ASP H 145 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 138 through 139
    Processing sheet with id=AB7, first strand: chain 'H' and resid 152 through 155
    Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 14
      removed outlier: 7.148A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   LYS L 107 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ALA L  13 " --> pdb=" O   LYS L 107 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA L  84 " --> pdb=" O   VAL L 104 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 114 through 118
      removed outlier: 6.082A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 145 through 150
      removed outlier: 3.666A  pdb=" N   VAL L 205 " --> pdb=" O   VAL L 196 " (cutoff:3.500A)

    254 hydrogen bonds defined for protein.
    630 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: 0.97

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        0.70 -     0.95: 1
        0.95 -     1.20: 0
        1.20 -     1.45: 3014
        1.45 -     1.70: 3736
        1.70 -     1.95: 29
  Bond restraints: 6780
  Sorted by residual:
  bond pdb=" CG  PRO L 119 "
       pdb=" CD  PRO L 119 "
    ideal  model  delta    sigma   weight residual
    1.503  0.703  0.800 3.40e-02 8.65e+02 5.53e+02
  bond pdb=" CB  PRO L 119 "
       pdb=" CG  PRO L 119 "
    ideal  model  delta    sigma   weight residual
    1.492  1.947 -0.455 5.00e-02 4.00e+02 8.28e+01
  bond pdb=" N   PRO L 119 "
       pdb=" CD  PRO L 119 "
    ideal  model  delta    sigma   weight residual
    1.473  1.599 -0.126 1.40e-02 5.10e+03 8.08e+01
  bond pdb=" N   PRO L 119 "
       pdb=" CA  PRO L 119 "
    ideal  model  delta    sigma   weight residual
    1.465  1.322  0.143 2.03e-02 2.43e+03 4.93e+01
  bond pdb=" CB  PRO H 214 "
       pdb=" CG  PRO H 214 "
    ideal  model  delta    sigma   weight residual
    1.492  1.632 -0.140 5.00e-02 4.00e+02 7.87e+00
  ... (remaining 6775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.21: 9217
        5.21 -    10.42: 14
       10.42 -    15.63: 1
       15.63 -    20.84: 1
       20.84 -    26.05: 2
  Bond angle restraints: 9235
  Sorted by residual:
  angle pdb=" N   PRO L 119 "
        pdb=" CD  PRO L 119 "
        pdb=" CG  PRO L 119 "
      ideal   model   delta    sigma   weight residual
     103.20   77.15   26.05 1.50e+00 4.44e-01 3.01e+02
  angle pdb=" CA  PRO L 119 "
        pdb=" CB  PRO L 119 "
        pdb=" CG  PRO L 119 "
      ideal   model   delta    sigma   weight residual
     104.50   83.94   20.56 1.90e+00 2.77e-01 1.17e+02
  angle pdb=" CA  PRO L 119 "
        pdb=" N   PRO L 119 "
        pdb=" CD  PRO L 119 "
      ideal   model   delta    sigma   weight residual
     112.00   96.85   15.15 1.40e+00 5.10e-01 1.17e+02
  angle pdb=" N   PRO L 119 "
        pdb=" CA  PRO L 119 "
        pdb=" CB  PRO L 119 "
      ideal   model   delta    sigma   weight residual
     103.08   95.32    7.76 9.70e-01 1.06e+00 6.40e+01
  angle pdb=" CB  PRO L 119 "
        pdb=" CG  PRO L 119 "
        pdb=" CD  PRO L 119 "
      ideal   model   delta    sigma   weight residual
     106.10   83.74   22.36 3.20e+00 9.77e-02 4.88e+01
  ... (remaining 9230 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 3424
       17.78 -    35.56: 505
       35.56 -    53.33: 111
       53.33 -    71.11: 18
       71.11 -    88.89: 10
  Dihedral angle restraints: 4068
    sinusoidal: 1545
      harmonic: 2523
  Sorted by residual:
  dihedral pdb=" CB  CYS H 141 "
           pdb=" SG  CYS H 141 "
           pdb=" SG  CYS H 197 "
           pdb=" CB  CYS H 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.64  -69.64     1      1.00e+01 1.00e-02 6.26e+01
  dihedral pdb=" CA  LYS B  50 "
           pdb=" C   LYS B  50 "
           pdb=" N   VAL B  51 "
           pdb=" CA  VAL B  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.17  -35.83     0      5.00e+00 4.00e-02 5.13e+01
  dihedral pdb=" CB  CYS A 140 "
           pdb=" SG  CYS A 140 "
           pdb=" SG  CYS A 195 "
           pdb=" CB  CYS A 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.51  -52.51     1      1.00e+01 1.00e-02 3.76e+01
  ... (remaining 4065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 808
       0.045 -    0.090: 171
       0.090 -    0.135: 79
       0.135 -    0.180: 0
       0.180 -    0.224: 1
  Chirality restraints: 1059
  Sorted by residual:
  chirality pdb=" CA  PRO L 119 "
            pdb=" N   PRO L 119 "
            pdb=" C   PRO L 119 "
            pdb=" CB  PRO L 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  PRO B 141 "
            pdb=" N   PRO B 141 "
            pdb=" C   PRO B 141 "
            pdb=" CB  PRO B 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  TYR B 140 "
            pdb=" N   TYR B 140 "
            pdb=" C   TYR B 140 "
            pdb=" CB  TYR B 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 1056 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE L 118 "   -0.097 5.00e-02 4.00e+02   1.35e-01 2.90e+01
        pdb=" N   PRO L 119 "    0.232 5.00e-02 4.00e+02
        pdb=" CA  PRO L 119 "   -0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO L 119 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 213 "   -0.093 5.00e-02 4.00e+02   1.34e-01 2.89e+01
        pdb=" N   PRO H 214 "    0.232 5.00e-02 4.00e+02
        pdb=" CA  PRO H 214 "   -0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO H 214 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  58 "    0.026 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO L  59 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO L  59 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO L  59 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 108
        2.62 -     3.19: 5850
        3.19 -     3.76: 10027
        3.76 -     4.33: 13368
        4.33 -     4.90: 22129
  Nonbonded interactions: 51482
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 182 "
            pdb=" OD1 ASP B 184 "
     model   vdw
     2.050 3.040
  nonbonded pdb=" OE1 GLN L 166 "
            pdb=" OG  SER L 171 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OG  SER B 201 "
            pdb=" O   SER B 203 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASN A  52 "
            pdb=" OH  TYR L  32 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" N   GLU H 149 "
            pdb=" OE1 GLU H 149 "
     model   vdw
     2.240 3.120
  ... (remaining 51477 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.810
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
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      :  0.012   0.800   6788  Z= 0.392
  Angle     :  0.809  26.045   9251  Z= 0.433
  Chirality :  0.044   0.224   1059
  Planarity :  0.007   0.135   1175
  Dihedral  : 17.378  88.887   2422
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.75 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 35.97 %
    Favored  : 63.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.30), residues: 859
  helix: -1.40 (0.75), residues: 36
  sheet:  0.44 (0.26), residues: 407
  loop : -0.55 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 108 
 TYR   0.020   0.001   TYR L 140 
 PHE   0.013   0.002   PHE L 118 
 TRP   0.025   0.002   TRP B 148 
 HIS   0.005   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.01245 ( 6780)
  covalent geometry    : angle       0.80853 ( 9235)
  SS BOND              : bond        0.00429 (    8)
  SS BOND              : angle       0.84596 (   16)
  hydrogen bonds       : bond        0.27395 (  237)
  hydrogen bonds       : angle      10.59559 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.8321 (mppt) cc_final: 0.7921 (mmpt)
REVERT: B  149 LYS cc_start: 0.7403 (tttm) cc_final: 0.6937 (tptp)
  outliers start: 1
  outliers final: 1
  residues processed: 151
  average time/residue: 0.0803
  time to fit residues: 16.3357
Evaluate side-chains
  147 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
H  39 GLN
H 172 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.151212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.109064 restraints weight = 9707.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.105338 restraints weight = 7967.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.107004 restraints weight = 7074.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.107477 restraints weight = 4857.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.108226 restraints weight = 4135.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6788  Z= 0.173
  Angle     :  0.662  10.605   9251  Z= 0.343
  Chirality :  0.045   0.158   1059
  Planarity :  0.005   0.078   1175
  Dihedral  :  5.034  38.835    929
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 32.02 %
    Favored  : 63.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.30), residues: 859
  helix: -1.60 (0.70), residues: 38
  sheet:  0.70 (0.26), residues: 416
  loop : -0.65 (0.34), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 108 
 TYR   0.014   0.001   TYR B 140 
 PHE   0.019   0.002   PHE B 135 
 TRP   0.015   0.001   TRP B 148 
 HIS   0.005   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 6780)
  covalent geometry    : angle       0.66208 ( 9235)
  SS BOND              : bond        0.00544 (    8)
  SS BOND              : angle       0.85331 (   16)
  hydrogen bonds       : bond        0.04286 (  237)
  hydrogen bonds       : angle       7.14120 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASN cc_start: 0.9195 (t0) cc_final: 0.8952 (t0)
REVERT: A  115 LYS cc_start: 0.8316 (mppt) cc_final: 0.7976 (mmtt)
REVERT: B  148 TRP cc_start: 0.8284 (m100) cc_final: 0.8018 (m100)
  outliers start: 36
  outliers final: 22
  residues processed: 187
  average time/residue: 0.0845
  time to fit residues: 20.8855
Evaluate side-chains
  165 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  166 THR
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:    9.9990
   chunk 80 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 166 GLN
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110258 restraints weight = 9666.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108728 restraints weight = 7217.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110459 restraints weight = 5862.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.110691 restraints weight = 3913.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110866 restraints weight = 3464.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6788  Z= 0.135
  Angle     :  0.630   7.222   9251  Z= 0.322
  Chirality :  0.044   0.154   1059
  Planarity :  0.005   0.061   1175
  Dihedral  :  4.840  38.833    927
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 32.41 %
    Favored  : 62.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.30), residues: 859
  helix: -1.58 (0.72), residues: 38
  sheet:  0.77 (0.26), residues: 410
  loop : -0.59 (0.33), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  24 
 TYR   0.014   0.001   TYR B 140 
 PHE   0.012   0.002   PHE B 135 
 TRP   0.012   0.001   TRP H  36 
 HIS   0.003   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6780)
  covalent geometry    : angle       0.62984 ( 9235)
  SS BOND              : bond        0.00467 (    8)
  SS BOND              : angle       0.78972 (   16)
  hydrogen bonds       : bond        0.03442 (  237)
  hydrogen bonds       : angle       6.40282 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 161
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.8993 (t80) cc_final: 0.8735 (t80)
REVERT: A  115 LYS cc_start: 0.8316 (mppt) cc_final: 0.8039 (mmtt)
REVERT: B  105 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7529 (pm20)
REVERT: B  108 ARG cc_start: 0.7584 (ptm-80) cc_final: 0.7371 (ptm-80)
REVERT: B  148 TRP cc_start: 0.8387 (m100) cc_final: 0.7974 (m100)
REVERT: H   72 ASP cc_start: 0.8103 (t0) cc_final: 0.7621 (t0)
REVERT: H  117 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7197 (pptt)
REVERT: L    3 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7751 (mt0)
REVERT: L   29 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8676 (t)
REVERT: L   82 ASP cc_start: 0.7785 (m-30) cc_final: 0.7474 (m-30)
REVERT: L  136 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8363 (pp)
  outliers start: 39
  outliers final: 25
  residues processed: 188
  average time/residue: 0.0900
  time to fit residues: 22.2576
Evaluate side-chains
  171 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  180 SER
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain L residue    3 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0010
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.7390

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

Flipped N/Q/H residues before XYZ refinement:
L 166 GLN
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.150713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.108783 restraints weight = 9775.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.103509 restraints weight = 8036.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.105447 restraints weight = 6538.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.106123 restraints weight = 4716.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.106308 restraints weight = 4085.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6788  Z= 0.197
  Angle     :  0.655   7.434   9251  Z= 0.334
  Chirality :  0.044   0.158   1059
  Planarity :  0.005   0.053   1175
  Dihedral  :  4.940  39.613    927
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  8.70 %
    Allowed  : 30.57 %
    Favored  : 60.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.30), residues: 859
  helix: -1.71 (0.75), residues: 38
  sheet:  0.74 (0.26), residues: 402
  loop : -0.55 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  61 
 TYR   0.012   0.001   TYR B 140 
 PHE   0.026   0.002   PHE L 139 
 TRP   0.015   0.002   TRP H  36 
 HIS   0.005   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6780)
  covalent geometry    : angle       0.65449 ( 9235)
  SS BOND              : bond        0.00554 (    8)
  SS BOND              : angle       1.03697 (   16)
  hydrogen bonds       : bond        0.03273 (  237)
  hydrogen bonds       : angle       6.05752 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 149
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9191 (t80) cc_final: 0.8989 (t80)
REVERT: A   86 ASP cc_start: 0.8610 (t0) cc_final: 0.8270 (t0)
REVERT: A  115 LYS cc_start: 0.8384 (mppt) cc_final: 0.8079 (mmtt)
REVERT: B  105 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7554 (pm20)
REVERT: H   38 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8508 (ptt90)
REVERT: H  117 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7297 (pptt)
REVERT: L    3 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7870 (mt0)
REVERT: L   47 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8698 (mp)
REVERT: L  119 PRO cc_start: 0.8977 (Cg_endo) cc_final: 0.8747 (Cg_exo)
REVERT: L  136 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8296 (pp)
REVERT: L  139 PHE cc_start: 0.8502 (p90) cc_final: 0.8296 (p90)
  outliers start: 66
  outliers final: 40
  residues processed: 197
  average time/residue: 0.0888
  time to fit residues: 22.9890
Evaluate side-chains
  180 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 134
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  142 LEU
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  166 THR
Chi-restraints excluded: chain H residue  170 VAL
Chi-restraints excluded: chain H residue  180 SER
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue    3 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.109785 restraints weight = 9770.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.107852 restraints weight = 7130.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.109215 restraints weight = 5746.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.110085 restraints weight = 3895.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.110116 restraints weight = 3612.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6788  Z= 0.139
  Angle     :  0.648   9.185   9251  Z= 0.328
  Chirality :  0.043   0.151   1059
  Planarity :  0.005   0.048   1175
  Dihedral  :  4.842  39.415    927
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 31.88 %
    Favored  : 61.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.30), residues: 859
  helix: -1.83 (0.75), residues: 38
  sheet:  0.87 (0.26), residues: 407
  loop : -0.51 (0.33), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  82B
 TYR   0.015   0.001   TYR B 140 
 PHE   0.018   0.002   PHE L 139 
 TRP   0.015   0.001   TRP B 148 
 HIS   0.003   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6780)
  covalent geometry    : angle       0.64726 ( 9235)
  SS BOND              : bond        0.00758 (    8)
  SS BOND              : angle       0.91468 (   16)
  hydrogen bonds       : bond        0.02908 (  237)
  hydrogen bonds       : angle       5.69841 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 146
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9138 (t80) cc_final: 0.8919 (t80)
REVERT: A   86 ASP cc_start: 0.8501 (t0) cc_final: 0.8110 (t70)
REVERT: A  115 LYS cc_start: 0.8357 (mppt) cc_final: 0.8085 (mmtt)
REVERT: B  105 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7475 (pm20)
REVERT: B  108 ARG cc_start: 0.7564 (ptm-80) cc_final: 0.7339 (ptm-80)
REVERT: B  170 ASP cc_start: 0.8742 (t0) cc_final: 0.8411 (t0)
REVERT: H   38 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8571 (ptt90)
REVERT: H  117 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7320 (pptt)
REVERT: L    3 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7739 (mt0)
REVERT: L  119 PRO cc_start: 0.8994 (Cg_endo) cc_final: 0.8785 (Cg_exo)
REVERT: L  136 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8256 (pp)
  outliers start: 47
  outliers final: 29
  residues processed: 181
  average time/residue: 0.0815
  time to fit residues: 19.7707
Evaluate side-chains
  167 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  170 VAL
Chi-restraints excluded: chain H residue  180 SER
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue    3 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  174 SER
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0040
   chunk 63 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.6000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.148070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.104433 restraints weight = 9967.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.102254 restraints weight = 6903.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.103301 restraints weight = 7190.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.105473 restraints weight = 4667.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.105501 restraints weight = 3479.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   6788  Z= 0.276
  Angle     :  0.707   9.409   9251  Z= 0.364
  Chirality :  0.045   0.149   1059
  Planarity :  0.005   0.046   1175
  Dihedral  :  5.184  40.473    927
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 30.96 %
    Favored  : 62.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.30), residues: 859
  helix: -1.74 (0.79), residues: 38
  sheet:  0.83 (0.26), residues: 402
  loop : -0.68 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  82B
 TYR   0.014   0.002   TYR B  87 
 PHE   0.023   0.002   PHE B 118 
 TRP   0.019   0.002   TRP H  36 
 HIS   0.005   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00637 ( 6780)
  covalent geometry    : angle       0.70527 ( 9235)
  SS BOND              : bond        0.00641 (    8)
  SS BOND              : angle       1.24124 (   16)
  hydrogen bonds       : bond        0.03264 (  237)
  hydrogen bonds       : angle       5.86357 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 140
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8045 (mt-10)
REVERT: A   53 TYR cc_start: 0.9306 (t80) cc_final: 0.8939 (t80)
REVERT: A   86 ASP cc_start: 0.8770 (t0) cc_final: 0.8459 (t0)
REVERT: A  115 LYS cc_start: 0.8440 (mppt) cc_final: 0.8120 (mmtt)
REVERT: H   38 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8493 (ptt90)
REVERT: H  117 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7390 (pptt)
REVERT: L   70 ASP cc_start: 0.8445 (m-30) cc_final: 0.8190 (p0)
REVERT: L  105 GLU cc_start: 0.8384 (mp0) cc_final: 0.8030 (mp0)
REVERT: L  119 PRO cc_start: 0.9085 (Cg_endo) cc_final: 0.8867 (Cg_exo)
REVERT: L  136 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8382 (pp)
  outliers start: 53
  outliers final: 40
  residues processed: 180
  average time/residue: 0.0862
  time to fit residues: 20.5623
Evaluate side-chains
  176 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 133
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASP
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  136 THR
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  170 VAL
Chi-restraints excluded: chain H residue  180 SER
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  174 SER
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.148650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.107759 restraints weight = 9715.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.104450 restraints weight = 8755.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.106163 restraints weight = 8367.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.106557 restraints weight = 5289.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.107399 restraints weight = 4594.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6788  Z= 0.133
  Angle     :  0.654   9.474   9251  Z= 0.329
  Chirality :  0.044   0.148   1059
  Planarity :  0.004   0.045   1175
  Dihedral  :  4.925  39.779    927
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 32.94 %
    Favored  : 61.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.30), residues: 859
  helix: -1.90 (0.75), residues: 37
  sheet:  0.84 (0.26), residues: 407
  loop : -0.56 (0.33), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 108 
 TYR   0.015   0.001   TYR B 140 
 PHE   0.017   0.002   PHE B 118 
 TRP   0.018   0.001   TRP B 148 
 HIS   0.003   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6780)
  covalent geometry    : angle       0.65320 ( 9235)
  SS BOND              : bond        0.00563 (    8)
  SS BOND              : angle       0.88365 (   16)
  hydrogen bonds       : bond        0.02849 (  237)
  hydrogen bonds       : angle       5.53024 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 146
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7798 (m-30)
REVERT: A   53 TYR cc_start: 0.9215 (t80) cc_final: 0.8918 (t80)
REVERT: B  108 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.7047 (ptm-80)
REVERT: B  170 ASP cc_start: 0.8406 (t0) cc_final: 0.8063 (t0)
REVERT: B  189 HIS cc_start: 0.8815 (m-70) cc_final: 0.8350 (m-70)
REVERT: B  211 ARG cc_start: 0.5045 (mmm-85) cc_final: 0.4616 (mtm180)
REVERT: H   38 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8641 (ptt90)
REVERT: H   72 ASP cc_start: 0.8132 (t0) cc_final: 0.7738 (t0)
REVERT: H  117 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7306 (pptt)
REVERT: L    3 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7671 (mt0)
REVERT: L  119 PRO cc_start: 0.9101 (Cg_endo) cc_final: 0.8886 (Cg_exo)
  outliers start: 42
  outliers final: 30
  residues processed: 174
  average time/residue: 0.0884
  time to fit residues: 20.4911
Evaluate side-chains
  165 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASP
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  170 VAL
Chi-restraints excluded: chain H residue  180 SER
Chi-restraints excluded: chain H residue  198 ASN
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    3 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  174 SER
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0870
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.5564

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.150432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.108088 restraints weight = 9841.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.105512 restraints weight = 6950.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.107077 restraints weight = 7690.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.107542 restraints weight = 4548.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.108280 restraints weight = 4045.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6788  Z= 0.184
  Angle     :  0.702  13.704   9251  Z= 0.351
  Chirality :  0.044   0.151   1059
  Planarity :  0.005   0.045   1175
  Dihedral  :  5.074  39.598    927
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 33.20 %
    Favored  : 60.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.30), residues: 859
  helix: -1.86 (0.77), residues: 37
  sheet:  0.84 (0.26), residues: 406
  loop : -0.60 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 155 
 TYR   0.012   0.001   TYR B 140 
 PHE   0.029   0.002   PHE B 118 
 TRP   0.018   0.002   TRP B 148 
 HIS   0.004   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6780)
  covalent geometry    : angle       0.70145 ( 9235)
  SS BOND              : bond        0.00575 (    8)
  SS BOND              : angle       1.02682 (   16)
  hydrogen bonds       : bond        0.02937 (  237)
  hydrogen bonds       : angle       5.52191 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 140
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9276 (t80) cc_final: 0.8854 (t80)
REVERT: B  108 ARG cc_start: 0.7755 (ptm-80) cc_final: 0.7502 (ptm-80)
REVERT: B  149 LYS cc_start: 0.7319 (tttm) cc_final: 0.6910 (tptp)
REVERT: B  170 ASP cc_start: 0.8725 (t0) cc_final: 0.8301 (t0)
REVERT: B  189 HIS cc_start: 0.8841 (m-70) cc_final: 0.8462 (m-70)
REVERT: B  211 ARG cc_start: 0.5203 (mmm-85) cc_final: 0.4728 (mtp85)
REVERT: H   38 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8505 (ptt90)
REVERT: H  117 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7390 (pptt)
REVERT: L  119 PRO cc_start: 0.9113 (Cg_endo) cc_final: 0.8867 (Cg_exo)
  outliers start: 46
  outliers final: 36
  residues processed: 175
  average time/residue: 0.0927
  time to fit residues: 21.5137
Evaluate side-chains
  173 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASP
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  166 THR
Chi-restraints excluded: chain H residue  170 VAL
Chi-restraints excluded: chain H residue  180 SER
Chi-restraints excluded: chain H residue  198 ASN
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  178 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110981 restraints weight = 9855.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.107344 restraints weight = 7246.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.109005 restraints weight = 6234.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.109595 restraints weight = 4202.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.110205 restraints weight = 3650.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6788  Z= 0.126
  Angle     :  0.709  11.956   9251  Z= 0.348
  Chirality :  0.044   0.149   1059
  Planarity :  0.005   0.045   1175
  Dihedral  :  4.975  39.316    927
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 34.12 %
    Favored  : 60.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.30), residues: 859
  helix: -1.99 (0.79), residues: 35
  sheet:  0.92 (0.26), residues: 405
  loop : -0.47 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 155 
 TYR   0.014   0.001   TYR B 140 
 PHE   0.025   0.002   PHE L 116 
 TRP   0.021   0.002   TRP B 148 
 HIS   0.002   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6780)
  covalent geometry    : angle       0.70903 ( 9235)
  SS BOND              : bond        0.00552 (    8)
  SS BOND              : angle       0.80636 (   16)
  hydrogen bonds       : bond        0.02755 (  237)
  hydrogen bonds       : angle       5.37849 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8026 (m-30)
REVERT: A   53 TYR cc_start: 0.9222 (t80) cc_final: 0.8789 (t80)
REVERT: A  115 LYS cc_start: 0.8258 (mmpt) cc_final: 0.7678 (mppt)
REVERT: B  108 ARG cc_start: 0.7739 (ptm-80) cc_final: 0.7456 (ptm-80)
REVERT: B  149 LYS cc_start: 0.7279 (tttm) cc_final: 0.6933 (tptp)
REVERT: B  170 ASP cc_start: 0.8751 (t0) cc_final: 0.8331 (t0)
REVERT: B  189 HIS cc_start: 0.8832 (m-70) cc_final: 0.8495 (m-70)
REVERT: B  211 ARG cc_start: 0.4990 (mmm-85) cc_final: 0.4528 (mtp85)
REVERT: H   38 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8503 (ptt90)
REVERT: H  117 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7210 (pptt)
REVERT: H  155 TRP cc_start: 0.7305 (m-90) cc_final: 0.6550 (m-90)
REVERT: L    3 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (mt0)
REVERT: L   36 TYR cc_start: 0.8941 (m-10) cc_final: 0.8336 (m-10)
REVERT: L  119 PRO cc_start: 0.9100 (Cg_endo) cc_final: 0.8836 (Cg_exo)
  outliers start: 39
  outliers final: 31
  residues processed: 169
  average time/residue: 0.0856
  time to fit residues: 19.2199
Evaluate side-chains
  169 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 134
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASP
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  166 THR
Chi-restraints excluded: chain H residue  170 VAL
Chi-restraints excluded: chain H residue  180 SER
Chi-restraints excluded: chain H residue  198 ASN
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    3 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  178 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.110847 restraints weight = 9736.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.107682 restraints weight = 6982.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.109159 restraints weight = 5708.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110008 restraints weight = 4408.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110104 restraints weight = 3927.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6788  Z= 0.128
  Angle     :  0.713  11.802   9251  Z= 0.351
  Chirality :  0.044   0.148   1059
  Planarity :  0.004   0.043   1175
  Dihedral  :  4.912  38.090    927
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 34.65 %
    Favored  : 61.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.30), residues: 859
  helix: -1.95 (0.79), residues: 35
  sheet:  0.91 (0.26), residues: 412
  loop : -0.55 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 155 
 TYR   0.012   0.001   TYR B 140 
 PHE   0.022   0.002   PHE L 118 
 TRP   0.020   0.002   TRP B 148 
 HIS   0.002   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6780)
  covalent geometry    : angle       0.71245 ( 9235)
  SS BOND              : bond        0.00556 (    8)
  SS BOND              : angle       0.95767 (   16)
  hydrogen bonds       : bond        0.02687 (  237)
  hydrogen bonds       : angle       5.27782 (  630)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9211 (t80) cc_final: 0.8932 (t80)
REVERT: A   81 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7450 (mt-10)
REVERT: A  115 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7665 (mppt)
REVERT: B    6 GLN cc_start: 0.8718 (mt0) cc_final: 0.8016 (pt0)
REVERT: B  102 THR cc_start: 0.9249 (p) cc_final: 0.9011 (p)
REVERT: B  108 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7426 (ptm-80)
REVERT: B  170 ASP cc_start: 0.8687 (t0) cc_final: 0.8299 (t0)
REVERT: B  189 HIS cc_start: 0.8872 (m-70) cc_final: 0.8463 (m-70)
REVERT: B  211 ARG cc_start: 0.4996 (mmm-85) cc_final: 0.4566 (mtp85)
REVERT: H   38 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8563 (ptt90)
REVERT: H  117 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7138 (pptt)
REVERT: H  155 TRP cc_start: 0.7241 (m-90) cc_final: 0.6597 (m-90)
REVERT: L    3 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7872 (mt0)
REVERT: L   36 TYR cc_start: 0.8911 (m-10) cc_final: 0.8284 (m-10)
  outliers start: 31
  outliers final: 28
  residues processed: 165
  average time/residue: 0.0850
  time to fit residues: 18.8942
Evaluate side-chains
  169 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASP
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  194 CYS
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LYS
Chi-restraints excluded: chain H residue  164 VAL
Chi-restraints excluded: chain H residue  166 THR
Chi-restraints excluded: chain H residue  198 ASN
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain L residue    3 GLN
Chi-restraints excluded: chain L residue   29 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  178 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0570
   chunk 11 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.3504

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.100796 restraints weight = 9769.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.104234 restraints weight = 5358.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.106380 restraints weight = 3666.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.107637 restraints weight = 2901.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.108572 restraints weight = 2517.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6788  Z= 0.168
  Angle     :  0.719  11.813   9251  Z= 0.357
  Chirality :  0.044   0.150   1059
  Planarity :  0.004   0.042   1175
  Dihedral  :  4.963  38.402    927
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 34.12 %
    Favored  : 61.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.30), residues: 859
  helix: -1.90 (0.80), residues: 35
  sheet:  0.87 (0.26), residues: 412
  loop : -0.55 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 155 
 TYR   0.013   0.001   TYR B 140 
 PHE   0.024   0.002   PHE B 135 
 TRP   0.020   0.002   TRP L 148 
 HIS   0.004   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6780)
  covalent geometry    : angle       0.71826 ( 9235)
  SS BOND              : bond        0.00586 (    8)
  SS BOND              : angle       1.08946 (   16)
  hydrogen bonds       : bond        0.02768 (  237)
  hydrogen bonds       : angle       5.32170 (  630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1243.05 seconds
wall clock time: 22 minutes 24.18 seconds (1344.18 seconds total)