Starting phenix.real_space_refine
on Sun Apr 27 01:50:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nt6_0503/04_2025/6nt6_0503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nt6_0503/04_2025/6nt6_0503.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nt6_0503/04_2025/6nt6_0503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nt6_0503/04_2025/6nt6_0503.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nt6_0503/04_2025/6nt6_0503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nt6_0503/04_2025/6nt6_0503.cif"
  }
  resolution = 4.0
  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=   0.005
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      36      5.16       5
     C    2712      2.51       5
     N     724      2.21       5
     O     726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4198
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2099
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 10, 'TRANS': 267}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 160
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 95
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.31, per 1000 atoms: 0.79
  Number of scatterers: 4198
  At special positions: 0
  Unit cell: (88.2, 61.32, 98.28, 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      36     16.00
     O     726      8.00
     N     724      7.00
     C    2712      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: 0.92
  Conformation dependent library (CDL) restraints added in 471.6 milliseconds
  

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1064

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 2 sheets defined
      67.3% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 41
    Processing helix  chain 'A' and resid 48 through 75
      removed outlier: 3.802A  pdb=" N   SER A  52 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLY A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   VAL A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU A  65 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 83
    Processing helix  chain 'A' and resid 88 through 95
      removed outlier: 4.129A  pdb=" N   PHE A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 111
      removed outlier: 4.579A  pdb=" N   ALA A 102 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LEU A 103 " --> pdb=" O   TRP A  99 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LEU A 104 " --> pdb=" O   TYR A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 140
      removed outlier: 3.715A  pdb=" N   LEU A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.553A  pdb=" N   SER A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 171
      removed outlier: 4.344A  pdb=" N   GLY A 163 " --> pdb=" O   ASN A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 188
      Proline residue:  A 178  - end of helix
      removed outlier: 4.432A  pdb=" N   LYS A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 4.008A  pdb=" N   SER A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLN A 278 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 306
      removed outlier: 3.697A  pdb=" N   SER A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 346
      removed outlier: 3.794A  pdb=" N   ILE A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 41
    Processing helix  chain 'B' and resid 48 through 75
      removed outlier: 3.802A  pdb=" N   SER B  52 " --> pdb=" O   PRO B  48 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLY B  63 " --> pdb=" O   ALA B  59 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   VAL B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 83
    Processing helix  chain 'B' and resid 88 through 95
      removed outlier: 4.129A  pdb=" N   PHE B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 111
      removed outlier: 4.580A  pdb=" N   ALA B 102 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LEU B 103 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU B 104 " --> pdb=" O   TYR B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 140
      removed outlier: 3.716A  pdb=" N   LEU B 139 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY B 140 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 156
      removed outlier: 3.553A  pdb=" N   SER B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 171
      removed outlier: 4.344A  pdb=" N   GLY B 163 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 188
      Proline residue:  B 178  - end of helix
      removed outlier: 4.432A  pdb=" N   LYS B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLU B 182 " --> pdb=" O   PRO B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 221
    Processing helix  chain 'B' and resid 269 through 279
      removed outlier: 4.007A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLN B 278 " --> pdb=" O   CYS B 274 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 306
      removed outlier: 3.697A  pdb=" N   SER B 306 " --> pdb=" O   ASP B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 346
      removed outlier: 3.793A  pdb=" N   ILE B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 226
      removed outlier: 4.469A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU A 264 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 205 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 226
      removed outlier: 4.470A  pdb=" N   SER B 248 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU B 264 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE B 205 " --> pdb=" O   ARG B 315 " (cutoff:3.500A)

    252 hydrogen bonds defined for protein.
    750 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: 1.00

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1336
        1.34 -     1.46: 730
        1.46 -     1.58: 2164
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 4270
  Sorted by residual:
  bond pdb=" CA  ALA A  47 "
       pdb=" C   ALA A  47 "
    ideal  model  delta    sigma   weight residual
    1.525  1.560 -0.035 2.10e-02 2.27e+03 2.74e+00
  bond pdb=" CA  ALA B  47 "
       pdb=" C   ALA B  47 "
    ideal  model  delta    sigma   weight residual
    1.525  1.559 -0.034 2.10e-02 2.27e+03 2.67e+00
  bond pdb=" CG  PRO B 269 "
       pdb=" CD  PRO B 269 "
    ideal  model  delta    sigma   weight residual
    1.503  1.465  0.038 3.40e-02 8.65e+02 1.27e+00
  bond pdb=" CG  PRO A 269 "
       pdb=" CD  PRO A 269 "
    ideal  model  delta    sigma   weight residual
    1.503  1.465  0.038 3.40e-02 8.65e+02 1.27e+00
  bond pdb=" CA  LEU A 177 "
       pdb=" C   LEU A 177 "
    ideal  model  delta    sigma   weight residual
    1.522  1.536 -0.014 1.26e-02 6.30e+03 1.19e+00
  ... (remaining 4265 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 5638
        1.97 -     3.94: 128
        3.94 -     5.91: 16
        5.91 -     7.88: 8
        7.88 -     9.85: 2
  Bond angle restraints: 5792
  Sorted by residual:
  angle pdb=" N   LEU A 177 "
        pdb=" CA  LEU A 177 "
        pdb=" C   LEU A 177 "
      ideal   model   delta    sigma   weight residual
     113.16  117.31   -4.15 1.42e+00 4.96e-01 8.53e+00
  angle pdb=" N   LEU B 177 "
        pdb=" CA  LEU B 177 "
        pdb=" C   LEU B 177 "
      ideal   model   delta    sigma   weight residual
     113.16  117.30   -4.14 1.42e+00 4.96e-01 8.52e+00
  angle pdb=" CA  ALA A  47 "
        pdb=" C   ALA A  47 "
        pdb=" N   PRO A  48 "
      ideal   model   delta    sigma   weight residual
     116.90  121.25   -4.35 1.50e+00 4.44e-01 8.39e+00
  angle pdb=" CA  ALA B  47 "
        pdb=" C   ALA B  47 "
        pdb=" N   PRO B  48 "
      ideal   model   delta    sigma   weight residual
     116.90  121.24   -4.34 1.50e+00 4.44e-01 8.37e+00
  angle pdb=" CA  LEU A 217 "
        pdb=" CB  LEU A 217 "
        pdb=" CG  LEU A 217 "
      ideal   model   delta    sigma   weight residual
     116.30  106.45    9.85 3.50e+00 8.16e-02 7.92e+00
  ... (remaining 5787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.10: 2278
       14.10 -    28.19: 242
       28.19 -    42.29: 34
       42.29 -    56.39: 6
       56.39 -    70.49: 4
  Dihedral angle restraints: 2564
    sinusoidal: 942
      harmonic: 1622
  Sorted by residual:
  dihedral pdb=" CA  SER B 268 "
           pdb=" C   SER B 268 "
           pdb=" N   PRO B 269 "
           pdb=" CA  PRO B 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.70  -20.30     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  SER A 268 "
           pdb=" C   SER A 268 "
           pdb=" N   PRO A 269 "
           pdb=" CA  PRO A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.73  -20.27     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ILE A  76 "
           pdb=" C   ILE A  76 "
           pdb=" N   PHE A  77 "
           pdb=" CA  PHE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.21  -17.79     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 2561 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 416
       0.032 -    0.063: 199
       0.063 -    0.095: 59
       0.095 -    0.127: 26
       0.127 -    0.158: 4
  Chirality restraints: 704
  Sorted by residual:
  chirality pdb=" CA  LEU B 177 "
            pdb=" N   LEU B 177 "
            pdb=" C   LEU B 177 "
            pdb=" CB  LEU B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  LEU A 177 "
            pdb=" N   LEU A 177 "
            pdb=" C   LEU A 177 "
            pdb=" CB  LEU A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  SER B 268 "
            pdb=" N   SER B 268 "
            pdb=" C   SER B 268 "
            pdb=" CB  SER B 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 701 not shown)

  Planarity restraints: 712
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  95 "    0.036 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO A  96 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A  96 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  96 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  95 "    0.036 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO B  96 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  96 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  96 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  18 "    0.034 5.00e-02 4.00e+02   5.11e-02 4.18e+00
        pdb=" N   PRO B  19 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B  19 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  19 "    0.028 5.00e-02 4.00e+02
  ... (remaining 709 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1309
        2.83 -     3.35: 3693
        3.35 -     3.87: 6331
        3.87 -     4.38: 6712
        4.38 -     4.90: 11611
  Nonbonded interactions: 29656
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 172 "
            pdb=" OE2 GLU B 265 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OH  TYR A 172 "
            pdb=" OE2 GLU A 265 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   LEU B 126 "
            pdb=" OG  SER B 129 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" O   LEU A 126 "
            pdb=" OG  SER A 129 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OH  TYR A 169 "
            pdb=" NZ  LYS A 174 "
     model   vdw
     2.332 3.120
  ... (remaining 29651 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             0.230
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.710
  Find NCS groups from input model:        0.080
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
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      :  0.005   0.038   4270  Z= 0.232
  Angle     :  0.795   9.850   5792  Z= 0.424
  Chirality :  0.043   0.158    704
  Planarity :  0.007   0.054    712
  Dihedral  : 11.988  70.486   1500
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  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: -3.32 (0.29), residues: 524
  helix: -1.69 (0.22), residues: 330
  sheet: -1.62 (0.63), residues: 56
  loop : -3.30 (0.37), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  99 
 HIS   0.005   0.001   HIS B 204 
 PHE   0.019   0.003   PHE A  95 
 TYR   0.008   0.002   TYR A 319 
 ARG   0.004   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13320 (  252)
  hydrogen bonds       : angle       6.75403 (  750)
  covalent geometry    : bond        0.00499 ( 4270)
  covalent geometry    : angle       0.79472 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8032 (mt) cc_final: 0.7717 (tp)
REVERT: A  148 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7831 (mt-10)
REVERT: A  158 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8499 (mttp)
REVERT: A  183 CYS cc_start: 0.8369 (m) cc_final: 0.8093 (m)
REVERT: A  302 ASP cc_start: 0.8483 (m-30) cc_final: 0.8239 (m-30)
REVERT: A  310 CYS cc_start: 0.8755 (m) cc_final: 0.8286 (m)
REVERT: B  105 LEU cc_start: 0.8034 (mt) cc_final: 0.7701 (tp)
REVERT: B  132 CYS cc_start: 0.7914 (m) cc_final: 0.7644 (m)
REVERT: B  148 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7694 (mt-10)
REVERT: B  151 GLU cc_start: 0.8732 (tt0) cc_final: 0.8502 (tm-30)
REVERT: B  158 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8430 (mttp)
REVERT: B  183 CYS cc_start: 0.8395 (m) cc_final: 0.8120 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1536
  time to fit residues: 28.4491
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.0050
   chunk 40 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   overall best weight:    2.3400

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 337 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 = 0.3587 r_free = 0.3587 target = 0.097788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.081272 restraints weight = 14629.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.083261 restraints weight = 8924.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.084644 restraints weight = 6382.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4270  Z= 0.142
  Angle     :  0.677   8.535   5792  Z= 0.322
  Chirality :  0.040   0.147    704
  Planarity :  0.005   0.038    712
  Dihedral  :  4.831  15.503    586
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.13 %
    Favored  : 82.03 %
  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: -0.87 (0.35), residues: 524
  helix:  0.57 (0.28), residues: 318
  sheet: -1.74 (0.64), residues: 56
  loop : -2.54 (0.42), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  99 
 HIS   0.004   0.001   HIS B  83 
 PHE   0.010   0.001   PHE A  95 
 TYR   0.006   0.001   TYR B 314 
 ARG   0.003   0.000   ARG B 315 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  252)
  hydrogen bonds       : angle       4.69889 (  750)
  covalent geometry    : bond        0.00311 ( 4270)
  covalent geometry    : angle       0.67699 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8080 (mt) cc_final: 0.7759 (tp)
REVERT: A  276 MET cc_start: 0.8212 (mtm) cc_final: 0.7899 (ttm)
REVERT: B  105 LEU cc_start: 0.8093 (mt) cc_final: 0.7765 (tp)
REVERT: B  148 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8016 (mt-10)
REVERT: B  158 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8276 (mttp)
REVERT: B  276 MET cc_start: 0.8139 (mtm) cc_final: 0.7886 (ttm)
  outliers start: 8
  outliers final: 4
  residues processed: 94
  average time/residue: 0.1275
  time to fit residues: 15.6888
Evaluate side-chains
  65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:   30.0000
   chunk 2 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0020
   chunk 34 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 42 optimal weight:   30.0000
   chunk 18 optimal weight:   10.0000
   overall best weight:    5.3996

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

Flipped N/Q/H residues before XYZ refinement:
** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
B 162 HIS
** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.094268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.078105 restraints weight = 14928.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.080157 restraints weight = 8572.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.081489 restraints weight = 5995.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4270  Z= 0.233
  Angle     :  0.771  10.949   5792  Z= 0.363
  Chirality :  0.042   0.158    704
  Planarity :  0.005   0.036    712
  Dihedral  :  4.923  21.348    586
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.89 %
    Favored  : 77.19 %
  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: -0.18 (0.36), residues: 524
  helix:  1.23 (0.28), residues: 324
  sheet: -1.78 (0.69), residues: 56
  loop : -2.58 (0.44), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  99 
 HIS   0.005   0.002   HIS A 337 
 PHE   0.008   0.001   PHE B  36 
 TYR   0.018   0.002   TYR B 319 
 ARG   0.003   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  252)
  hydrogen bonds       : angle       4.61937 (  750)
  covalent geometry    : bond        0.00507 ( 4270)
  covalent geometry    : angle       0.77076 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7942 (mt) cc_final: 0.7570 (tp)
REVERT: A  276 MET cc_start: 0.8243 (mtm) cc_final: 0.7940 (ttm)
REVERT: A  308 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8424 (mttt)
REVERT: B   70 CYS cc_start: 0.8735 (m) cc_final: 0.8331 (t)
REVERT: B  105 LEU cc_start: 0.8007 (mt) cc_final: 0.7655 (tp)
REVERT: B  158 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8209 (mttp)
REVERT: B  276 MET cc_start: 0.8211 (mtm) cc_final: 0.7921 (ttm)
  outliers start: 17
  outliers final: 14
  residues processed: 84
  average time/residue: 0.1766
  time to fit residues: 20.2740
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 7 optimal weight:   30.0000
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
A 162 HIS
** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.095554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.079499 restraints weight = 14617.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.081518 restraints weight = 8525.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082957 restraints weight = 5956.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   4270  Z= 0.142
  Angle     :  0.670  12.055   5792  Z= 0.307
  Chirality :  0.039   0.147    704
  Planarity :  0.004   0.029    712
  Dihedral  :  4.734  26.673    586
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.12 %
    Favored  : 77.42 %
  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:  0.29 (0.37), residues: 524
  helix:  1.68 (0.29), residues: 322
  sheet: -1.68 (0.71), residues: 56
  loop : -2.48 (0.43), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 166 
 HIS   0.002   0.001   HIS B 204 
 PHE   0.007   0.001   PHE B  95 
 TYR   0.009   0.001   TYR B 314 
 ARG   0.003   0.000   ARG A 315 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03279 (  252)
  hydrogen bonds       : angle       4.26045 (  750)
  covalent geometry    : bond        0.00324 ( 4270)
  covalent geometry    : angle       0.66970 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7960 (mt) cc_final: 0.7594 (tp)
REVERT: A  143 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7948 (ptpt)
REVERT: A  159 ASN cc_start: 0.8332 (t0) cc_final: 0.7982 (t0)
REVERT: A  319 TYR cc_start: 0.9085 (p90) cc_final: 0.8709 (p90)
REVERT: B  105 LEU cc_start: 0.8039 (mt) cc_final: 0.7695 (tp)
REVERT: B  158 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8112 (mttp)
REVERT: B  271 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8341 (mt0)
  outliers start: 15
  outliers final: 8
  residues processed: 82
  average time/residue: 0.1665
  time to fit residues: 18.3131
Evaluate side-chains
  65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue  271 GLN
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 18 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 8 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   overall best weight:    7.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 HIS
** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.092298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.076788 restraints weight = 15376.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.078558 restraints weight = 9125.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.079817 restraints weight = 6489.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   4270  Z= 0.297
  Angle     :  0.820  12.348   5792  Z= 0.388
  Chirality :  0.042   0.127    704
  Planarity :  0.005   0.035    712
  Dihedral  :  5.073  25.138    586
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 22.35 %
    Favored  : 72.12 %
  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: -0.15 (0.37), residues: 524
  helix:  1.33 (0.28), residues: 322
  sheet: -1.88 (0.69), residues: 56
  loop : -2.63 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  99 
 HIS   0.004   0.002   HIS B 204 
 PHE   0.017   0.002   PHE B  95 
 TYR   0.013   0.002   TYR B 319 
 ARG   0.003   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  252)
  hydrogen bonds       : angle       4.81799 (  750)
  covalent geometry    : bond        0.00645 ( 4270)
  covalent geometry    : angle       0.81972 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8020 (mt) cc_final: 0.7627 (tp)
REVERT: A  159 ASN cc_start: 0.8325 (t0) cc_final: 0.7839 (t0)
REVERT: A  271 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8498 (mt0)
REVERT: A  319 TYR cc_start: 0.9101 (p90) cc_final: 0.8793 (p90)
REVERT: B  158 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8143 (mttp)
REVERT: B  271 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8620 (mt0)
  outliers start: 24
  outliers final: 18
  residues processed: 73
  average time/residue: 0.1288
  time to fit residues: 12.5964
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain B residue  271 GLN
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 HIS
** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 337 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 = 0.3535 r_free = 0.3535 target = 0.094738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.079752 restraints weight = 14692.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.081658 restraints weight = 8630.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.082967 restraints weight = 6054.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4270  Z= 0.145
  Angle     :  0.649  10.727   5792  Z= 0.301
  Chirality :  0.038   0.141    704
  Planarity :  0.004   0.035    712
  Dihedral  :  4.709  21.963    586
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.12 %
    Favored  : 71.20 %
  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:  0.34 (0.37), residues: 524
  helix:  1.71 (0.29), residues: 322
  sheet: -1.83 (0.69), residues: 56
  loop : -2.36 (0.46), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.002   0.001   HIS B  84 
 PHE   0.011   0.001   PHE B  95 
 TYR   0.011   0.001   TYR B 314 
 ARG   0.002   0.000   ARG A 315 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03220 (  252)
  hydrogen bonds       : angle       4.30654 (  750)
  covalent geometry    : bond        0.00330 ( 4270)
  covalent geometry    : angle       0.64898 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8004 (mt) cc_final: 0.7646 (tp)
REVERT: A  159 ASN cc_start: 0.8363 (t0) cc_final: 0.7872 (t0)
REVERT: A  276 MET cc_start: 0.8107 (ttm) cc_final: 0.7903 (tmm)
REVERT: B  105 LEU cc_start: 0.8011 (mt) cc_final: 0.7667 (tp)
REVERT: B  158 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8113 (mttp)
  outliers start: 16
  outliers final: 10
  residues processed: 75
  average time/residue: 0.1228
  time to fit residues: 12.6737
Evaluate side-chains
  67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
** B 337 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 = 0.3547 r_free = 0.3547 target = 0.095315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.079840 restraints weight = 14901.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.081696 restraints weight = 8884.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.083021 restraints weight = 6295.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4270  Z= 0.138
  Angle     :  0.651   9.379   5792  Z= 0.304
  Chirality :  0.038   0.136    704
  Planarity :  0.004   0.032    712
  Dihedral  :  4.635  24.837    586
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.12 %
    Favored  : 71.20 %
  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:  0.49 (0.38), residues: 524
  helix:  1.86 (0.29), residues: 322
  sheet: -2.10 (0.67), residues: 60
  loop : -2.20 (0.48), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 337 
 PHE   0.014   0.001   PHE B 284 
 TYR   0.026   0.002   TYR A 319 
 ARG   0.001   0.000   ARG B 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03083 (  252)
  hydrogen bonds       : angle       4.18822 (  750)
  covalent geometry    : bond        0.00317 ( 4270)
  covalent geometry    : angle       0.65094 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7982 (mt) cc_final: 0.7622 (tp)
REVERT: A  159 ASN cc_start: 0.8404 (t0) cc_final: 0.7836 (t0)
REVERT: A  308 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8407 (mttt)
REVERT: B  105 LEU cc_start: 0.7983 (mt) cc_final: 0.7635 (tp)
REVERT: B  158 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8126 (mttp)
  outliers start: 16
  outliers final: 12
  residues processed: 79
  average time/residue: 0.1252
  time to fit residues: 13.3383
Evaluate side-chains
  71 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  271 GLN
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 28 optimal weight:   30.0000
   chunk 48 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 42 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 337 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.094600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.079178 restraints weight = 14617.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.081103 restraints weight = 8825.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.082430 restraints weight = 6231.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.4379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4270  Z= 0.170
  Angle     :  0.677   9.454   5792  Z= 0.320
  Chirality :  0.039   0.130    704
  Planarity :  0.004   0.032    712
  Dihedral  :  4.656  24.570    586
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.35 %
    Favored  : 70.97 %
  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:  0.44 (0.38), residues: 524
  helix:  1.82 (0.29), residues: 322
  sheet: -2.12 (0.67), residues: 60
  loop : -2.23 (0.46), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 166 
 HIS   0.002   0.001   HIS A 337 
 PHE   0.014   0.002   PHE B  95 
 TYR   0.027   0.002   TYR A 319 
 ARG   0.001   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03298 (  252)
  hydrogen bonds       : angle       4.29003 (  750)
  covalent geometry    : bond        0.00388 ( 4270)
  covalent geometry    : angle       0.67735 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8017 (mt) cc_final: 0.7639 (tp)
REVERT: A  159 ASN cc_start: 0.8351 (t0) cc_final: 0.7815 (t0)
REVERT: B  158 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8116 (mttp)
  outliers start: 16
  outliers final: 14
  residues processed: 69
  average time/residue: 0.1069
  time to fit residues: 10.2442
Evaluate side-chains
  69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  271 GLN
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 51 optimal weight:    0.2980
   chunk 21 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.097259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.081463 restraints weight = 14880.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.083480 restraints weight = 9064.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.084820 restraints weight = 6434.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4270  Z= 0.108
  Angle     :  0.637   7.812   5792  Z= 0.294
  Chirality :  0.037   0.143    704
  Planarity :  0.003   0.032    712
  Dihedral  :  4.363  23.959    586
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 26.73 %
    Favored  : 70.74 %
  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:  0.72 (0.38), residues: 524
  helix:  2.05 (0.29), residues: 322
  sheet: -1.96 (0.69), residues: 60
  loop : -2.18 (0.46), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.003   0.000   HIS A 337 
 PHE   0.007   0.001   PHE B  95 
 TYR   0.025   0.002   TYR A 319 
 ARG   0.002   0.000   ARG B 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02661 (  252)
  hydrogen bonds       : angle       3.95460 (  750)
  covalent geometry    : bond        0.00247 ( 4270)
  covalent geometry    : angle       0.63692 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7978 (mt) cc_final: 0.7628 (tp)
REVERT: A  159 ASN cc_start: 0.8303 (t0) cc_final: 0.7727 (t0)
REVERT: A  308 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8404 (mttt)
REVERT: B  105 LEU cc_start: 0.7995 (mt) cc_final: 0.7683 (tp)
REVERT: B  158 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8096 (mttp)
REVERT: B  308 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8267 (mmtp)
  outliers start: 11
  outliers final: 9
  residues processed: 74
  average time/residue: 0.1188
  time to fit residues: 12.2246
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 = 0.3556 r_free = 0.3556 target = 0.096245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.080604 restraints weight = 14804.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.082574 restraints weight = 8964.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.083869 restraints weight = 6369.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4270  Z= 0.125
  Angle     :  0.652   9.254   5792  Z= 0.296
  Chirality :  0.037   0.136    704
  Planarity :  0.004   0.033    712
  Dihedral  :  4.372  23.328    586
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 27.65 %
    Favored  : 70.05 %
  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:  0.85 (0.38), residues: 524
  helix:  2.14 (0.29), residues: 324
  sheet: -1.93 (0.70), residues: 60
  loop : -2.15 (0.46), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 337 
 PHE   0.011   0.001   PHE A  95 
 TYR   0.026   0.002   TYR A 319 
 ARG   0.001   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02793 (  252)
  hydrogen bonds       : angle       3.94562 (  750)
  covalent geometry    : bond        0.00289 ( 4270)
  covalent geometry    : angle       0.65159 ( 5792)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8082 (mt) cc_final: 0.7708 (tp)
REVERT: A  159 ASN cc_start: 0.8338 (t0) cc_final: 0.7756 (t0)
REVERT: A  308 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8445 (mttt)
REVERT: B  105 LEU cc_start: 0.8023 (mt) cc_final: 0.7716 (tp)
REVERT: B  158 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8086 (mttp)
REVERT: B  308 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8276 (mmtp)
  outliers start: 10
  outliers final: 9
  residues processed: 69
  average time/residue: 0.2634
  time to fit residues: 25.5798
Evaluate side-chains
  68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 3.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  303 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.095306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.079453 restraints weight = 15396.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.081441 restraints weight = 9209.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.082777 restraints weight = 6585.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4270  Z= 0.157
  Angle     :  0.699   9.046   5792  Z= 0.317
  Chirality :  0.039   0.152    704
  Planarity :  0.004   0.033    712
  Dihedral  :  4.423  22.839    586
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 27.19 %
    Favored  : 70.74 %
  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:  0.76 (0.38), residues: 524
  helix:  2.06 (0.29), residues: 326
  sheet: -2.17 (0.68), residues: 60
  loop : -2.11 (0.47), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 166 
 HIS   0.002   0.001   HIS B 204 
 PHE   0.014   0.002   PHE A  95 
 TYR   0.027   0.002   TYR A 319 
 ARG   0.001   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03054 (  252)
  hydrogen bonds       : angle       4.13439 (  750)
  covalent geometry    : bond        0.00360 ( 4270)
  covalent geometry    : angle       0.69872 ( 5792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1904.76 seconds
wall clock time: 35 minutes 16.85 seconds (2116.85 seconds total)