Starting phenix.real_space_refine
on Wed Feb 12 00:42:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7shs_25135/02_2025/7shs_25135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7shs_25135/02_2025/7shs_25135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7shs_25135/02_2025/7shs_25135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7shs_25135/02_2025/7shs_25135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7shs_25135/02_2025/7shs_25135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7shs_25135/02_2025/7shs_25135.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.038
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      48      5.16       5
     C    4545      2.51       5
     N    1092      2.21       5
     O    1188      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6873
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2291
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 8, 'TRANS': 274}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 3.97, per 1000 atoms: 0.58
  Number of scatterers: 6873
  At special positions: 0
  Unit cell: (90.96, 81.864, 84.138, 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      48     16.00
     O    1188      8.00
     N    1092      7.00
     C    4545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.71
  Conformation dependent library (CDL) restraints added in 971.8 milliseconds
  

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      76.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 20
    Processing helix  chain 'A' and resid 26 through 53
    Processing helix  chain 'A' and resid 63 through 68
      removed outlier: 3.615A  pdb=" N   TYR A  67 " --> pdb=" O   PHE A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 71
      No H-bonds generated for 'chain 'A' and resid 69 through 71'
    Processing helix  chain 'A' and resid 72 through 95
      removed outlier: 3.807A  pdb=" N   GLY A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LYS A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
      removed outlier: 3.574A  pdb=" N   MET A 117 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 131
      removed outlier: 3.843A  pdb=" N   LEU A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 159
      removed outlier: 3.743A  pdb=" N   CYS A 139 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU A 158 " --> pdb=" O   GLU A 154 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY A 159 " --> pdb=" O   PHE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 164 through 199
      removed outlier: 3.920A  pdb=" N   TYR A 168 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 222
    Processing helix  chain 'A' and resid 224 through 233
      removed outlier: 3.845A  pdb=" N   LEU A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 269
      removed outlier: 3.587A  pdb=" N   ALA A 248 " --> pdb=" O   TRP A 244 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   CYS A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 283
    Processing helix  chain 'B' and resid 15 through 20
    Processing helix  chain 'B' and resid 26 through 53
    Processing helix  chain 'B' and resid 63 through 68
      removed outlier: 3.615A  pdb=" N   TYR B  67 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 71
      No H-bonds generated for 'chain 'B' and resid 69 through 71'
    Processing helix  chain 'B' and resid 72 through 95
      removed outlier: 3.807A  pdb=" N   GLY B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LYS B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 117
      removed outlier: 3.574A  pdb=" N   MET B 117 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 131
      removed outlier: 3.844A  pdb=" N   LEU B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 159
      removed outlier: 3.744A  pdb=" N   CYS B 139 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER B 140 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B 159 " --> pdb=" O   PHE B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 163
    Processing helix  chain 'B' and resid 164 through 199
      removed outlier: 3.920A  pdb=" N   TYR B 168 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 222
    Processing helix  chain 'B' and resid 224 through 233
      removed outlier: 3.846A  pdb=" N   LEU B 228 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 269
      removed outlier: 3.587A  pdb=" N   ALA B 248 " --> pdb=" O   TRP B 244 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 283
    Processing helix  chain 'C' and resid 15 through 20
    Processing helix  chain 'C' and resid 26 through 53
    Processing helix  chain 'C' and resid 63 through 68
      removed outlier: 3.615A  pdb=" N   TYR C  67 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 71
      No H-bonds generated for 'chain 'C' and resid 69 through 71'
    Processing helix  chain 'C' and resid 72 through 95
      removed outlier: 3.808A  pdb=" N   GLY C  87 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LYS C  88 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 117
      removed outlier: 3.573A  pdb=" N   MET C 117 " --> pdb=" O   ALA C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 131
      removed outlier: 3.844A  pdb=" N   LEU C 131 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 159
      removed outlier: 3.744A  pdb=" N   CYS C 139 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER C 140 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU C 158 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY C 159 " --> pdb=" O   PHE C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 163
    Processing helix  chain 'C' and resid 164 through 199
      removed outlier: 3.920A  pdb=" N   TYR C 168 " --> pdb=" O   ARG C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 222
    Processing helix  chain 'C' and resid 224 through 233
      removed outlier: 3.845A  pdb=" N   LEU C 228 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 269
      removed outlier: 3.588A  pdb=" N   ALA C 248 " --> pdb=" O   TRP C 244 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS C 259 " --> pdb=" O   VAL C 255 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 283

    447 hydrogen bonds defined for protein.
    1323 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.79

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2076
        1.35 -     1.46: 2092
        1.46 -     1.58: 2864
        1.58 -     1.70: 0
        1.70 -     1.81: 72
  Bond restraints: 7104
  Sorted by residual:
  bond pdb=" CB  MET C  82 "
       pdb=" CG  MET C  82 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.93e-01
  bond pdb=" CB  MET A  82 "
       pdb=" CG  MET A  82 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.90e-01
  bond pdb=" CB  MET B  82 "
       pdb=" CG  MET B  82 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.49e-01
  bond pdb=" C   CYS B 120 "
       pdb=" N   PRO B 121 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 1.36e-02 5.41e+03 7.28e-01
  bond pdb=" CB  MET C 186 "
       pdb=" CG  MET C 186 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.21e-01
  ... (remaining 7099 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 9402
        1.82 -     3.65: 201
        3.65 -     5.47: 24
        5.47 -     7.30: 12
        7.30 -     9.12: 21
  Bond angle restraints: 9660
  Sorted by residual:
  angle pdb=" CB  MET B  82 "
        pdb=" CG  MET B  82 "
        pdb=" SD  MET B  82 "
      ideal   model   delta    sigma   weight residual
     112.70  121.82   -9.12 3.00e+00 1.11e-01 9.25e+00
  angle pdb=" CB  MET A  82 "
        pdb=" CG  MET A  82 "
        pdb=" SD  MET A  82 "
      ideal   model   delta    sigma   weight residual
     112.70  121.80   -9.10 3.00e+00 1.11e-01 9.21e+00
  angle pdb=" CB  MET C  82 "
        pdb=" CG  MET C  82 "
        pdb=" SD  MET C  82 "
      ideal   model   delta    sigma   weight residual
     112.70  121.79   -9.09 3.00e+00 1.11e-01 9.17e+00
  angle pdb=" CB  MET B  16 "
        pdb=" CG  MET B  16 "
        pdb=" SD  MET B  16 "
      ideal   model   delta    sigma   weight residual
     112.70  120.62   -7.92 3.00e+00 1.11e-01 6.97e+00
  angle pdb=" CB  MET A  16 "
        pdb=" CG  MET A  16 "
        pdb=" SD  MET A  16 "
      ideal   model   delta    sigma   weight residual
     112.70  120.62   -7.92 3.00e+00 1.11e-01 6.96e+00
  ... (remaining 9655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3602
       17.70 -    35.40: 301
       35.40 -    53.11: 36
       53.11 -    70.81: 6
       70.81 -    88.51: 12
  Dihedral angle restraints: 3957
    sinusoidal: 1491
      harmonic: 2466
  Sorted by residual:
  dihedral pdb=" CA  ASP B 272 "
           pdb=" C   ASP B 272 "
           pdb=" N   GLU B 273 "
           pdb=" CA  GLU B 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.06  -15.94     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  ASP C 272 "
           pdb=" C   ASP C 272 "
           pdb=" N   GLU C 273 "
           pdb=" CA  GLU C 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.09  -15.91     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  ASP A 272 "
           pdb=" C   ASP A 272 "
           pdb=" N   GLU A 273 "
           pdb=" CA  GLU A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.10  -15.90     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 624
       0.029 -    0.058: 212
       0.058 -    0.087: 129
       0.087 -    0.116: 31
       0.116 -    0.145: 9
  Chirality restraints: 1005
  Sorted by residual:
  chirality pdb=" CA  ASP A 253 "
            pdb=" N   ASP A 253 "
            pdb=" C   ASP A 253 "
            pdb=" CB  ASP A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  ASP B 253 "
            pdb=" N   ASP B 253 "
            pdb=" C   ASP B 253 "
            pdb=" CB  ASP B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  ASP C 253 "
            pdb=" N   ASP C 253 "
            pdb=" C   ASP C 253 "
            pdb=" CB  ASP C 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1002 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 223 "    0.014 2.00e-02 2.50e+03   1.49e-02 5.51e+00
        pdb=" CG  TRP C 223 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 223 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 223 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 223 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 223 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 223 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 223 "    0.014 2.00e-02 2.50e+03   1.48e-02 5.50e+00
        pdb=" CG  TRP B 223 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 223 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 223 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 223 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 223 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 223 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 223 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 223 "   -0.014 2.00e-02 2.50e+03   1.47e-02 5.39e+00
        pdb=" CG  TRP A 223 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 223 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 223 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 223 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 223 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 223 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 2536
        2.86 -     3.37: 7146
        3.37 -     3.88: 11704
        3.88 -     4.39: 12583
        4.39 -     4.90: 21034
  Nonbonded interactions: 55003
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  69 "
            pdb=" N   ARG B 136 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" O   ASP A 242 "
            pdb=" OG1 THR A 245 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   ASP C 242 "
            pdb=" OG1 THR C 245 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   ASP B 242 "
            pdb=" OG1 THR B 245 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" OE1 GLN C 192 "
            pdb=" NH2 ARG C 195 "
     model   vdw
     2.388 3.120
  ... (remaining 54998 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.280
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7104  Z= 0.174
  Angle     :  0.740   9.123   9660  Z= 0.370
  Chirality :  0.040   0.145   1005
  Planarity :  0.005   0.050   1206
  Dihedral  : 13.648  88.509   2397
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.27), residues: 843
  helix:  0.85 (0.20), residues: 615
  sheet:  None (None), residues: 0
  loop : -0.26 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP C 223 
 HIS   0.001   0.000   HIS C 210 
 PHE   0.014   0.001   PHE C 276 
 TYR   0.026   0.001   TYR A 156 
 ARG   0.002   0.000   ARG B  55 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8266 (pmm) cc_final: 0.7989 (ppp)
REVERT: A  126 ASP cc_start: 0.8657 (t0) cc_final: 0.8269 (t0)
REVERT: A  158 GLU cc_start: 0.8676 (tp30) cc_final: 0.8259 (tm-30)
REVERT: A  177 TRP cc_start: 0.8306 (m100) cc_final: 0.8093 (m100)
REVERT: A  250 CYS cc_start: 0.8771 (m) cc_final: 0.8270 (m)
REVERT: B   34 TRP cc_start: 0.6187 (m-10) cc_final: 0.5752 (m100)
REVERT: B  182 TYR cc_start: 0.6720 (t80) cc_final: 0.6194 (t80)
REVERT: B  240 ILE cc_start: 0.7110 (pt) cc_final: 0.6806 (tp)
REVERT: B  246 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7445 (pp20)
REVERT: B  254 ILE cc_start: 0.8982 (mm) cc_final: 0.8611 (mm)
REVERT: B  260 TYR cc_start: 0.7404 (t80) cc_final: 0.7027 (t80)
REVERT: C   70 GLU cc_start: 0.8353 (pm20) cc_final: 0.7873 (pm20)
REVERT: C   72 ASN cc_start: 0.8193 (m-40) cc_final: 0.7823 (m-40)
REVERT: C  130 GLN cc_start: 0.8802 (mm110) cc_final: 0.8102 (mm110)
REVERT: C  246 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7804 (mm-30)
REVERT: C  251 VAL cc_start: 0.9084 (m) cc_final: 0.8870 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2287
  time to fit residues: 65.3957
Evaluate side-chains
  125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0020
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   overall best weight:    2.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
B   9 GLN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
C 249 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.075803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.067646 restraints weight = 30269.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.069478 restraints weight = 18313.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.070806 restraints weight = 12418.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7104  Z= 0.212
  Angle     :  0.577   6.791   9660  Z= 0.307
  Chirality :  0.040   0.139   1005
  Planarity :  0.005   0.049   1206
  Dihedral  :  3.982  18.617    942
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.13 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.29), residues: 843
  helix:  1.72 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop :  0.65 (0.44), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 230 
 HIS   0.004   0.001   HIS C 249 
 PHE   0.021   0.002   PHE B 226 
 TYR   0.018   0.002   TYR C 193 
 ARG   0.004   0.001   ARG C 164 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8532 (pmm) cc_final: 0.8093 (ppp)
REVERT: A  126 ASP cc_start: 0.9024 (t0) cc_final: 0.8732 (t0)
REVERT: A  131 LEU cc_start: 0.9381 (tp) cc_final: 0.9106 (tp)
REVERT: A  250 CYS cc_start: 0.8521 (m) cc_final: 0.8300 (m)
REVERT: B   34 TRP cc_start: 0.6318 (m-10) cc_final: 0.5783 (m100)
REVERT: B   40 LEU cc_start: 0.9104 (mp) cc_final: 0.8505 (tp)
REVERT: B   82 MET cc_start: 0.8461 (ttp) cc_final: 0.8011 (ttp)
REVERT: B  110 ASN cc_start: 0.8797 (p0) cc_final: 0.7948 (p0)
REVERT: B  117 MET cc_start: 0.8800 (mmp) cc_final: 0.8389 (mmm)
REVERT: B  210 HIS cc_start: 0.7363 (m90) cc_final: 0.7065 (m90)
REVERT: B  246 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7523 (pp20)
REVERT: B  257 LYS cc_start: 0.8200 (mptt) cc_final: 0.7900 (mmmm)
REVERT: B  260 TYR cc_start: 0.7527 (t80) cc_final: 0.6939 (t80)
REVERT: C   71 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: C   72 ASN cc_start: 0.8523 (m-40) cc_final: 0.8015 (m-40)
REVERT: C   88 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8235 (mtmm)
REVERT: C   94 LEU cc_start: 0.7848 (mt) cc_final: 0.7188 (mt)
REVERT: C  130 GLN cc_start: 0.8801 (mm110) cc_final: 0.8067 (mm110)
REVERT: C  131 LEU cc_start: 0.9212 (tp) cc_final: 0.8945 (tp)
REVERT: C  171 TYR cc_start: 0.7627 (t80) cc_final: 0.7211 (t80)
REVERT: C  175 CYS cc_start: 0.8787 (m) cc_final: 0.8212 (p)
REVERT: C  246 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8103 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1534
  time to fit residues: 33.2530
Evaluate side-chains
  109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.074838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.066950 restraints weight = 33123.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.068875 restraints weight = 19462.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.070197 restraints weight = 12832.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7104  Z= 0.202
  Angle     :  0.565   6.506   9660  Z= 0.299
  Chirality :  0.040   0.140   1005
  Planarity :  0.004   0.053   1206
  Dihedral  :  3.999  18.672    942
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.56 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.30), residues: 843
  helix:  1.73 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop :  0.57 (0.46), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 177 
 HIS   0.006   0.001   HIS C 249 
 PHE   0.016   0.002   PHE B 226 
 TYR   0.019   0.002   TYR C  46 
 ARG   0.003   0.001   ARG C 132 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8599 (pmm) cc_final: 0.8154 (ppp)
REVERT: A  126 ASP cc_start: 0.9052 (t0) cc_final: 0.8747 (t0)
REVERT: A  131 LEU cc_start: 0.9427 (tp) cc_final: 0.9116 (tp)
REVERT: B   10 MET cc_start: 0.8522 (mtm) cc_final: 0.8192 (mmt)
REVERT: B   34 TRP cc_start: 0.6143 (m-10) cc_final: 0.5803 (m100)
REVERT: B   40 LEU cc_start: 0.9168 (mp) cc_final: 0.8819 (tp)
REVERT: B   82 MET cc_start: 0.8536 (ttp) cc_final: 0.8059 (ttm)
REVERT: B  108 PHE cc_start: 0.7902 (t80) cc_final: 0.7529 (t80)
REVERT: B  110 ASN cc_start: 0.8662 (p0) cc_final: 0.7674 (t0)
REVERT: B  117 MET cc_start: 0.8867 (mmp) cc_final: 0.8399 (mmm)
REVERT: B  123 LEU cc_start: 0.9342 (mt) cc_final: 0.8949 (tt)
REVERT: B  210 HIS cc_start: 0.7268 (m90) cc_final: 0.6865 (m170)
REVERT: B  257 LYS cc_start: 0.8281 (mptt) cc_final: 0.7971 (mmmm)
REVERT: B  260 TYR cc_start: 0.7608 (t80) cc_final: 0.7200 (t80)
REVERT: C   82 MET cc_start: 0.8543 (ttp) cc_final: 0.8183 (ttp)
REVERT: C   88 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8274 (mtmm)
REVERT: C   94 LEU cc_start: 0.7735 (mt) cc_final: 0.7064 (mt)
REVERT: C  108 PHE cc_start: 0.7745 (t80) cc_final: 0.7311 (t80)
REVERT: C  117 MET cc_start: 0.8694 (mmp) cc_final: 0.7627 (tpp)
REVERT: C  130 GLN cc_start: 0.8712 (mm110) cc_final: 0.7970 (mm110)
REVERT: C  148 MET cc_start: 0.8811 (ttp) cc_final: 0.8544 (ttm)
REVERT: C  171 TYR cc_start: 0.8090 (t80) cc_final: 0.7135 (t80)
REVERT: C  175 CYS cc_start: 0.8834 (m) cc_final: 0.8570 (p)
REVERT: C  230 TRP cc_start: 0.8697 (t60) cc_final: 0.7313 (t60)
REVERT: C  260 TYR cc_start: 0.7635 (t80) cc_final: 0.7424 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1437
  time to fit residues: 29.8251
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 GLN
C 165 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.069075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.061271 restraints weight = 32843.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.063013 restraints weight = 19201.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.064284 restraints weight = 12845.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.6017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7104  Z= 0.322
  Angle     :  0.663   7.317   9660  Z= 0.366
  Chirality :  0.044   0.141   1005
  Planarity :  0.005   0.050   1206
  Dihedral  :  4.677  23.921    942
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.13 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.29), residues: 843
  helix:  1.35 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.41 (0.45), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 177 
 HIS   0.010   0.002   HIS C 249 
 PHE   0.018   0.002   PHE B 214 
 TYR   0.026   0.003   TYR C  46 
 ARG   0.005   0.001   ARG C 235 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 133
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8560 (pmm) cc_final: 0.8137 (ppp)
REVERT: A  126 ASP cc_start: 0.8995 (t0) cc_final: 0.8738 (t0)
REVERT: A  131 LEU cc_start: 0.9425 (tp) cc_final: 0.9059 (tp)
REVERT: A  176 PHE cc_start: 0.8688 (t80) cc_final: 0.8395 (t80)
REVERT: B    9 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7242 (pp30)
REVERT: B   10 MET cc_start: 0.8040 (mtm) cc_final: 0.7618 (mmt)
REVERT: B   86 PHE cc_start: 0.8881 (t80) cc_final: 0.8470 (t80)
REVERT: B  108 PHE cc_start: 0.8105 (t80) cc_final: 0.7863 (t80)
REVERT: B  110 ASN cc_start: 0.8450 (p0) cc_final: 0.8052 (t0)
REVERT: B  117 MET cc_start: 0.8734 (mmp) cc_final: 0.8227 (mmm)
REVERT: B  260 TYR cc_start: 0.7423 (t80) cc_final: 0.7080 (t80)
REVERT: C   82 MET cc_start: 0.8552 (ttp) cc_final: 0.8155 (ttp)
REVERT: C   88 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8131 (mtmm)
REVERT: C   94 LEU cc_start: 0.7812 (mt) cc_final: 0.6931 (mt)
REVERT: C  108 PHE cc_start: 0.7858 (t80) cc_final: 0.7527 (t80)
REVERT: C  130 GLN cc_start: 0.8593 (mm110) cc_final: 0.7841 (mm110)
REVERT: C  171 TYR cc_start: 0.8464 (t80) cc_final: 0.8098 (t80)
REVERT: C  175 CYS cc_start: 0.8960 (m) cc_final: 0.8658 (p)
REVERT: C  246 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8216 (mm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1548
  time to fit residues: 29.3694
Evaluate side-chains
  106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  33 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.071728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.064200 restraints weight = 32615.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.066063 restraints weight = 18802.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.067319 restraints weight = 12277.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.6042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7104  Z= 0.185
  Angle     :  0.562   7.478   9660  Z= 0.298
  Chirality :  0.040   0.131   1005
  Planarity :  0.004   0.045   1206
  Dihedral  :  4.204  20.336    942
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.29), residues: 843
  helix:  1.71 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.69 (0.45), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 223 
 HIS   0.006   0.001   HIS C 249 
 PHE   0.013   0.002   PHE B 226 
 TYR   0.016   0.002   TYR C  46 
 ARG   0.002   0.000   ARG C 164 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ARG cc_start: 0.5911 (mmt180) cc_final: 0.5058 (tpp-160)
REVERT: A  126 ASP cc_start: 0.8955 (t0) cc_final: 0.8664 (t0)
REVERT: A  131 LEU cc_start: 0.9422 (tp) cc_final: 0.9050 (tp)
REVERT: A  176 PHE cc_start: 0.8658 (t80) cc_final: 0.8432 (t80)
REVERT: A  257 LYS cc_start: 0.9065 (mptt) cc_final: 0.8740 (mmtm)
REVERT: B  108 PHE cc_start: 0.8342 (t80) cc_final: 0.8043 (t80)
REVERT: B  110 ASN cc_start: 0.8264 (p0) cc_final: 0.7991 (t0)
REVERT: B  117 MET cc_start: 0.8764 (mmp) cc_final: 0.8373 (mmm)
REVERT: B  260 TYR cc_start: 0.7345 (t80) cc_final: 0.7037 (t80)
REVERT: C   16 MET cc_start: 0.8483 (mmp) cc_final: 0.7772 (tpp)
REVERT: C   82 MET cc_start: 0.8497 (ttp) cc_final: 0.8182 (ttp)
REVERT: C   88 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8102 (mtmm)
REVERT: C   94 LEU cc_start: 0.7679 (mt) cc_final: 0.7090 (mt)
REVERT: C  108 PHE cc_start: 0.7666 (t80) cc_final: 0.7372 (t80)
REVERT: C  117 MET cc_start: 0.8467 (mmp) cc_final: 0.7454 (tpp)
REVERT: C  125 TYR cc_start: 0.8427 (t80) cc_final: 0.8131 (t80)
REVERT: C  130 GLN cc_start: 0.8641 (mm110) cc_final: 0.7976 (mm110)
REVERT: C  148 MET cc_start: 0.8859 (ttp) cc_final: 0.8532 (ttp)
REVERT: C  171 TYR cc_start: 0.8525 (t80) cc_final: 0.8074 (t80)
REVERT: C  175 CYS cc_start: 0.9061 (m) cc_final: 0.8733 (p)
REVERT: C  176 PHE cc_start: 0.8896 (t80) cc_final: 0.8463 (t80)
REVERT: C  246 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8181 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1750
  time to fit residues: 32.5532
Evaluate side-chains
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0060
   chunk 49 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7402

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 192 GLN
C 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.075336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.067565 restraints weight = 31507.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.069470 restraints weight = 18192.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.070776 restraints weight = 11913.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.6063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7104  Z= 0.134
  Angle     :  0.527   7.572   9660  Z= 0.271
  Chirality :  0.038   0.143   1005
  Planarity :  0.003   0.050   1206
  Dihedral  :  3.816  16.245    942
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.30), residues: 843
  helix:  1.91 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop :  0.86 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 223 
 HIS   0.006   0.001   HIS B  33 
 PHE   0.016   0.001   PHE C 173 
 TYR   0.018   0.001   TYR A 156 
 ARG   0.004   0.000   ARG B  60 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ARG cc_start: 0.6132 (mmt180) cc_final: 0.5398 (tpp-160)
REVERT: A  126 ASP cc_start: 0.8975 (t0) cc_final: 0.8616 (t0)
REVERT: A  131 LEU cc_start: 0.9456 (tp) cc_final: 0.9079 (tp)
REVERT: B   86 PHE cc_start: 0.8685 (t80) cc_final: 0.8389 (t80)
REVERT: B  108 PHE cc_start: 0.8481 (t80) cc_final: 0.7763 (t80)
REVERT: B  110 ASN cc_start: 0.8194 (p0) cc_final: 0.7737 (t0)
REVERT: B  117 MET cc_start: 0.8719 (mmp) cc_final: 0.8376 (mmm)
REVERT: B  127 LEU cc_start: 0.8734 (tt) cc_final: 0.8364 (tp)
REVERT: B  260 TYR cc_start: 0.7348 (t80) cc_final: 0.6768 (t80)
REVERT: C   17 ASP cc_start: 0.7763 (m-30) cc_final: 0.7024 (t0)
REVERT: C   82 MET cc_start: 0.8411 (ttp) cc_final: 0.7998 (ttp)
REVERT: C   88 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8100 (mtmm)
REVERT: C   94 LEU cc_start: 0.7608 (mt) cc_final: 0.6933 (mt)
REVERT: C  108 PHE cc_start: 0.7551 (t80) cc_final: 0.7213 (t80)
REVERT: C  117 MET cc_start: 0.8422 (mmp) cc_final: 0.7256 (tpp)
REVERT: C  123 LEU cc_start: 0.9243 (tt) cc_final: 0.8946 (tt)
REVERT: C  125 TYR cc_start: 0.8288 (t80) cc_final: 0.7992 (t80)
REVERT: C  127 LEU cc_start: 0.9135 (tt) cc_final: 0.8732 (mt)
REVERT: C  130 GLN cc_start: 0.8599 (mm110) cc_final: 0.7907 (mm110)
REVERT: C  171 TYR cc_start: 0.8517 (t80) cc_final: 0.8039 (t80)
REVERT: C  175 CYS cc_start: 0.9083 (m) cc_final: 0.8763 (p)
REVERT: C  176 PHE cc_start: 0.8754 (t80) cc_final: 0.8400 (t80)
REVERT: C  246 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8103 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1542
  time to fit residues: 29.7167
Evaluate side-chains
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
B   9 GLN
B  78 ASN
C   3 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.072752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.065450 restraints weight = 31638.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.067215 restraints weight = 17933.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.068399 restraints weight = 11850.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.6320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7104  Z= 0.183
  Angle     :  0.561   8.374   9660  Z= 0.296
  Chirality :  0.040   0.141   1005
  Planarity :  0.004   0.051   1206
  Dihedral  :  3.871  17.129    942
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.99 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.30), residues: 843
  helix:  1.72 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.64 (0.47), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 223 
 HIS   0.006   0.001   HIS C 210 
 PHE   0.012   0.001   PHE C 173 
 TYR   0.018   0.002   TYR A 156 
 ARG   0.002   0.000   ARG B  55 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8553 (pmm) cc_final: 0.8174 (ppp)
REVERT: A   55 ARG cc_start: 0.5949 (mmt180) cc_final: 0.5129 (tpp-160)
REVERT: A  126 ASP cc_start: 0.9043 (t0) cc_final: 0.8734 (t0)
REVERT: A  131 LEU cc_start: 0.9444 (tp) cc_final: 0.9034 (tp)
REVERT: A  250 CYS cc_start: 0.8419 (m) cc_final: 0.8087 (m)
REVERT: B    9 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7599 (pp30)
REVERT: B   86 PHE cc_start: 0.8713 (t80) cc_final: 0.8408 (t80)
REVERT: B  108 PHE cc_start: 0.8490 (t80) cc_final: 0.8194 (t80)
REVERT: B  117 MET cc_start: 0.8814 (mmp) cc_final: 0.8395 (mmm)
REVERT: B  260 TYR cc_start: 0.7221 (t80) cc_final: 0.6920 (t80)
REVERT: C    3 HIS cc_start: 0.4398 (OUTLIER) cc_final: 0.4198 (m-70)
REVERT: C   10 MET cc_start: 0.7380 (mmt) cc_final: 0.6980 (mmt)
REVERT: C   17 ASP cc_start: 0.7840 (m-30) cc_final: 0.7174 (t0)
REVERT: C   53 THR cc_start: 0.6923 (t) cc_final: 0.6613 (p)
REVERT: C   70 GLU cc_start: 0.8789 (pm20) cc_final: 0.8530 (pm20)
REVERT: C   82 MET cc_start: 0.8501 (ttp) cc_final: 0.8256 (ttp)
REVERT: C   88 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8076 (mtmm)
REVERT: C   94 LEU cc_start: 0.7675 (mt) cc_final: 0.6816 (mt)
REVERT: C  108 PHE cc_start: 0.7681 (t80) cc_final: 0.7203 (t80)
REVERT: C  117 MET cc_start: 0.8507 (mmp) cc_final: 0.7354 (tpp)
REVERT: C  123 LEU cc_start: 0.9239 (tt) cc_final: 0.8946 (tt)
REVERT: C  125 TYR cc_start: 0.8298 (t80) cc_final: 0.7962 (t80)
REVERT: C  127 LEU cc_start: 0.9259 (tt) cc_final: 0.8789 (mt)
REVERT: C  130 GLN cc_start: 0.8655 (mm110) cc_final: 0.7952 (mm110)
REVERT: C  148 MET cc_start: 0.8854 (ttp) cc_final: 0.8542 (ppp)
REVERT: C  171 TYR cc_start: 0.8704 (t80) cc_final: 0.8103 (t80)
REVERT: C  175 CYS cc_start: 0.9087 (m) cc_final: 0.8645 (p)
REVERT: C  176 PHE cc_start: 0.8939 (t80) cc_final: 0.8457 (t80)
REVERT: C  246 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8198 (mm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1481
  time to fit residues: 28.5900
Evaluate side-chains
  114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.071742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.064424 restraints weight = 32289.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.066144 restraints weight = 18056.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.067365 restraints weight = 11957.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.6549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7104  Z= 0.198
  Angle     :  0.578   8.708   9660  Z= 0.307
  Chirality :  0.041   0.158   1005
  Planarity :  0.004   0.051   1206
  Dihedral  :  4.035  18.491    942
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.29), residues: 843
  helix:  1.78 (0.21), residues: 591
  sheet:  None (None), residues: 0
  loop :  0.67 (0.44), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C  34 
 HIS   0.008   0.001   HIS C 210 
 PHE   0.018   0.002   PHE C 104 
 TYR   0.020   0.002   TYR A 156 
 ARG   0.002   0.000   ARG C 235 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8585 (pmm) cc_final: 0.8238 (ppp)
REVERT: A  126 ASP cc_start: 0.8961 (t0) cc_final: 0.8690 (t0)
REVERT: A  131 LEU cc_start: 0.9451 (tp) cc_final: 0.9040 (tp)
REVERT: A  176 PHE cc_start: 0.8554 (t80) cc_final: 0.8293 (t80)
REVERT: B   86 PHE cc_start: 0.8723 (t80) cc_final: 0.8422 (t80)
REVERT: B  117 MET cc_start: 0.8753 (mmp) cc_final: 0.8267 (mmm)
REVERT: B  260 TYR cc_start: 0.7377 (t80) cc_final: 0.7042 (t80)
REVERT: C   17 ASP cc_start: 0.7939 (m-30) cc_final: 0.7281 (t0)
REVERT: C   82 MET cc_start: 0.8497 (ttp) cc_final: 0.8229 (ttp)
REVERT: C   88 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8136 (mtmm)
REVERT: C   94 LEU cc_start: 0.7628 (mt) cc_final: 0.7093 (mm)
REVERT: C  108 PHE cc_start: 0.7767 (t80) cc_final: 0.7288 (t80)
REVERT: C  117 MET cc_start: 0.8492 (mmp) cc_final: 0.7446 (tpp)
REVERT: C  127 LEU cc_start: 0.9244 (tt) cc_final: 0.8995 (tt)
REVERT: C  130 GLN cc_start: 0.8661 (mm110) cc_final: 0.7981 (mm110)
REVERT: C  148 MET cc_start: 0.8869 (ttp) cc_final: 0.8503 (ppp)
REVERT: C  171 TYR cc_start: 0.8804 (t80) cc_final: 0.8175 (t80)
REVERT: C  175 CYS cc_start: 0.9093 (m) cc_final: 0.8748 (p)
REVERT: C  176 PHE cc_start: 0.9002 (t80) cc_final: 0.8528 (t80)
REVERT: C  246 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8325 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1432
  time to fit residues: 27.4224
Evaluate side-chains
  106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0030
   overall best weight:    3.1998

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.071323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.064008 restraints weight = 32749.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.065840 restraints weight = 18480.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.067014 restraints weight = 12024.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.6786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7104  Z= 0.229
  Angle     :  0.617   8.895   9660  Z= 0.328
  Chirality :  0.042   0.142   1005
  Planarity :  0.004   0.051   1206
  Dihedral  :  4.127  19.320    942
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.29), residues: 843
  helix:  1.71 (0.21), residues: 591
  sheet:  None (None), residues: 0
  loop :  0.56 (0.44), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C  34 
 HIS   0.008   0.001   HIS C 249 
 PHE   0.017   0.002   PHE A 276 
 TYR   0.028   0.002   TYR B 156 
 ARG   0.003   0.001   ARG B 162 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8603 (pmm) cc_final: 0.8249 (ppp)
REVERT: A  126 ASP cc_start: 0.8955 (t0) cc_final: 0.8699 (t0)
REVERT: A  131 LEU cc_start: 0.9458 (tp) cc_final: 0.9075 (tp)
REVERT: A  250 CYS cc_start: 0.8233 (m) cc_final: 0.7930 (m)
REVERT: B   82 MET cc_start: 0.8543 (ttm) cc_final: 0.8303 (ttm)
REVERT: B  117 MET cc_start: 0.8754 (mmp) cc_final: 0.8324 (mmm)
REVERT: B  260 TYR cc_start: 0.7387 (t80) cc_final: 0.7060 (t80)
REVERT: C   17 ASP cc_start: 0.7878 (m-30) cc_final: 0.7225 (t0)
REVERT: C   53 THR cc_start: 0.7039 (t) cc_final: 0.6733 (p)
REVERT: C   70 GLU cc_start: 0.8682 (pm20) cc_final: 0.8460 (pm20)
REVERT: C   82 MET cc_start: 0.8549 (ttp) cc_final: 0.8240 (ttp)
REVERT: C   88 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8141 (mtmm)
REVERT: C   94 LEU cc_start: 0.7641 (mt) cc_final: 0.7331 (mt)
REVERT: C  108 PHE cc_start: 0.7839 (t80) cc_final: 0.7393 (t80)
REVERT: C  117 MET cc_start: 0.8525 (mmp) cc_final: 0.7452 (tpp)
REVERT: C  123 LEU cc_start: 0.9235 (tt) cc_final: 0.8962 (tt)
REVERT: C  125 TYR cc_start: 0.8052 (t80) cc_final: 0.7704 (t80)
REVERT: C  127 LEU cc_start: 0.9209 (tt) cc_final: 0.8743 (mt)
REVERT: C  130 GLN cc_start: 0.8684 (mm110) cc_final: 0.7919 (mm110)
REVERT: C  171 TYR cc_start: 0.8819 (t80) cc_final: 0.8165 (t80)
REVERT: C  175 CYS cc_start: 0.9070 (m) cc_final: 0.8781 (p)
REVERT: C  250 CYS cc_start: 0.8923 (m) cc_final: 0.8422 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1543
  time to fit residues: 27.2177
Evaluate side-chains
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.074210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.066661 restraints weight = 32519.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.068573 restraints weight = 18477.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.069796 restraints weight = 12110.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.6681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7104  Z= 0.145
  Angle     :  0.559   8.393   9660  Z= 0.289
  Chirality :  0.040   0.154   1005
  Planarity :  0.004   0.050   1206
  Dihedral  :  3.850  17.096    942
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.30), residues: 843
  helix:  1.82 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  0.65 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C  34 
 HIS   0.003   0.001   HIS C 249 
 PHE   0.024   0.001   PHE B 217 
 TYR   0.016   0.001   TYR B 156 
 ARG   0.005   0.000   ARG C 112 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ARG cc_start: 0.6133 (mmt180) cc_final: 0.5184 (tpp-160)
REVERT: A  126 ASP cc_start: 0.8924 (t0) cc_final: 0.8612 (t0)
REVERT: A  131 LEU cc_start: 0.9463 (tp) cc_final: 0.9099 (tp)
REVERT: A  176 PHE cc_start: 0.8563 (t80) cc_final: 0.8257 (t80)
REVERT: B    9 GLN cc_start: 0.7909 (pp30) cc_final: 0.7530 (pp30)
REVERT: B  117 MET cc_start: 0.8640 (mmp) cc_final: 0.8254 (mmm)
REVERT: B  119 THR cc_start: 0.7786 (p) cc_final: 0.7407 (p)
REVERT: B  123 LEU cc_start: 0.9440 (mt) cc_final: 0.9171 (mt)
REVERT: B  127 LEU cc_start: 0.8793 (tt) cc_final: 0.8518 (tp)
REVERT: B  260 TYR cc_start: 0.7317 (t80) cc_final: 0.6779 (t80)
REVERT: C   17 ASP cc_start: 0.7690 (m-30) cc_final: 0.7171 (t0)
REVERT: C   70 GLU cc_start: 0.8642 (pm20) cc_final: 0.8280 (pm20)
REVERT: C   82 MET cc_start: 0.8516 (ttp) cc_final: 0.8072 (ttp)
REVERT: C   88 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8231 (mtmm)
REVERT: C  108 PHE cc_start: 0.7715 (t80) cc_final: 0.7346 (t80)
REVERT: C  111 TYR cc_start: 0.8915 (m-10) cc_final: 0.8639 (m-10)
REVERT: C  117 MET cc_start: 0.8441 (mmp) cc_final: 0.7266 (tpp)
REVERT: C  123 LEU cc_start: 0.9234 (tt) cc_final: 0.8938 (tt)
REVERT: C  125 TYR cc_start: 0.8076 (t80) cc_final: 0.7715 (t80)
REVERT: C  127 LEU cc_start: 0.9198 (tt) cc_final: 0.8737 (mt)
REVERT: C  130 GLN cc_start: 0.8606 (mm110) cc_final: 0.7917 (mm110)
REVERT: C  171 TYR cc_start: 0.8781 (t80) cc_final: 0.8150 (t80)
REVERT: C  175 CYS cc_start: 0.9073 (m) cc_final: 0.8775 (p)
REVERT: C  176 PHE cc_start: 0.8931 (t80) cc_final: 0.8494 (t80)
REVERT: C  235 ARG cc_start: 0.7414 (mmp80) cc_final: 0.6866 (mmp80)
REVERT: C  246 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8267 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1581
  time to fit residues: 28.2195
Evaluate side-chains
  108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0980
   chunk 34 optimal weight:    7.9990
   chunk 66 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.074340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.066945 restraints weight = 32429.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.068839 restraints weight = 18247.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.070015 restraints weight = 11847.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.6635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7104  Z= 0.139
  Angle     :  0.545   8.551   9660  Z= 0.279
  Chirality :  0.039   0.132   1005
  Planarity :  0.004   0.051   1206
  Dihedral  :  3.705  15.402    942
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.30), residues: 843
  helix:  1.78 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.45 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  34 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.030   0.001   PHE B  86 
 TYR   0.024   0.001   TYR A 156 
 ARG   0.003   0.000   ARG C 112 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1788.81 seconds
wall clock time: 32 minutes 57.32 seconds (1977.32 seconds total)