Starting phenix.real_space_refine
on Tue Mar  3 12:22:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nt6_0503/03_2026/6nt6_0503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nt6_0503/03_2026/6nt6_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nt6_0503/03_2026/6nt6_0503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nt6_0503/03_2026/6nt6_0503.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nt6_0503/03_2026/6nt6_0503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nt6_0503/03_2026/6nt6_0503.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'GLU:plan': 5, 'TRP:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 95
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.23, per 1000 atoms: 0.29
  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: 0.32
  Conformation dependent library (CDL) restraints added in 124.8 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: 0.16
  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: 0.59

  Time building geometry restraints manager: 0.46 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: 0.01
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:             0.380
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.020
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.880
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.001   ARG A 294 
 TYR   0.008   0.002   TYR A 319 
 PHE   0.019   0.003   PHE A  95 
 TRP   0.009   0.002   TRP A  99 
 HIS   0.005   0.001   HIS B 204 

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

*********************** 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  : 0.165 
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: 0.8121 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0653
  time to fit residues: 12.2831
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  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3545 r_free = 0.3545 target = 0.096047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.079784 restraints weight = 14763.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.081900 restraints weight = 8494.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.083290 restraints weight = 5879.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.084247 restraints weight = 4573.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.085045 restraints weight = 3832.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4270  Z= 0.231
  Angle     :  0.762   8.725   5792  Z= 0.366
  Chirality :  0.042   0.144    704
  Planarity :  0.005   0.041    712
  Dihedral  :  5.031  16.430    586
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.43 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.35), residues: 524
  helix:  0.61 (0.28), residues: 320
  sheet: -1.78 (0.64), residues: 56
  loop : -2.61 (0.41), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 315 
 TYR   0.007   0.002   TYR B 226 
 PHE   0.014   0.002   PHE A  95 
 TRP   0.006   0.001   TRP A 166 
 HIS   0.006   0.002   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 4270)
  covalent geometry    : angle       0.76181 ( 5792)
  hydrogen bonds       : bond        0.04112 (  252)
  hydrogen bonds       : angle       4.92129 (  750)

*********************** 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
  95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7994 (mt) cc_final: 0.7633 (tp)
REVERT: A  276 MET cc_start: 0.8182 (mtm) cc_final: 0.7859 (ttm)
REVERT: B   70 CYS cc_start: 0.8682 (m) cc_final: 0.8259 (t)
REVERT: B  105 LEU cc_start: 0.8068 (mt) cc_final: 0.7710 (tp)
REVERT: B  148 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7885 (mt-10)
REVERT: B  151 GLU cc_start: 0.8650 (tt0) cc_final: 0.8440 (tm-30)
REVERT: B  158 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8479 (mttp)
REVERT: B  276 MET cc_start: 0.8151 (mtm) cc_final: 0.7948 (ttm)
  outliers start: 12
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0555
  time to fit residues: 6.8670
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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   66 LEU
Chi-restraints excluded: chain A residue  150 SER
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  303 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 42 optimal weight:   30.0000
   chunk 7 optimal weight:   30.0000
   chunk 12 optimal weight:    8.9990
   overall best weight:    4.3990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.094872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.078435 restraints weight = 15265.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.080460 restraints weight = 9040.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.081829 restraints weight = 6378.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.082720 restraints weight = 5065.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.083449 restraints weight = 4329.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4270  Z= 0.191
  Angle     :  0.713  11.851   5792  Z= 0.337
  Chirality :  0.040   0.161    704
  Planarity :  0.004   0.034    712
  Dihedral  :  4.877  18.059    586
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.97 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.37), residues: 524
  helix:  1.41 (0.29), residues: 322
  sheet: -1.80 (0.70), residues: 56
  loop : -2.52 (0.43), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 315 
 TYR   0.020   0.002   TYR B 319 
 PHE   0.009   0.001   PHE B  95 
 TRP   0.005   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4270)
  covalent geometry    : angle       0.71266 ( 5792)
  hydrogen bonds       : bond        0.03850 (  252)
  hydrogen bonds       : angle       4.52752 (  750)

*********************** 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: 10
    poor density    : 77
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7961 (mt) cc_final: 0.7578 (tp)
REVERT: A  133 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8673 (mt0)
REVERT: A  319 TYR cc_start: 0.9114 (p90) cc_final: 0.8783 (p90)
REVERT: B   70 CYS cc_start: 0.8682 (m) cc_final: 0.8256 (t)
REVERT: B  105 LEU cc_start: 0.7993 (mt) cc_final: 0.7629 (tp)
REVERT: B  148 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8011 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 86
  average time/residue: 0.0569
  time to fit residues: 6.5122
Evaluate side-chains
  65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
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   66 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain B residue  130 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 1 optimal weight:   30.0000
   chunk 9 optimal weight:   10.0000
   chunk 34 optimal weight:   40.0000
   chunk 36 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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 133 GLN
** 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 = 0.3528 r_free = 0.3528 target = 0.094790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.079144 restraints weight = 14592.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.081111 restraints weight = 8587.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.082480 restraints weight = 5991.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.083387 restraints weight = 4676.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.083893 restraints weight = 3936.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4270  Z= 0.177
  Angle     :  0.698  12.632   5792  Z= 0.325
  Chirality :  0.039   0.143    704
  Planarity :  0.004   0.035    712
  Dihedral  :  4.821  20.164    586
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.58 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.37), residues: 524
  helix:  1.59 (0.29), residues: 324
  sheet: -1.90 (0.70), residues: 56
  loop : -2.52 (0.45), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 315 
 TYR   0.011   0.002   TYR A 319 
 PHE   0.010   0.001   PHE B  95 
 TRP   0.006   0.001   TRP A  99 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 4270)
  covalent geometry    : angle       0.69786 ( 5792)
  hydrogen bonds       : bond        0.03516 (  252)
  hydrogen bonds       : angle       4.49370 (  750)

*********************** 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
  80 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7991 (mt) cc_final: 0.7592 (tp)
REVERT: A  143 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8020 (ptpt)
REVERT: A  159 ASN cc_start: 0.8533 (t0) cc_final: 0.8169 (t0)
REVERT: A  319 TYR cc_start: 0.9124 (p90) cc_final: 0.8814 (p90)
REVERT: B  105 LEU cc_start: 0.7965 (mt) cc_final: 0.7600 (tp)
  outliers start: 17
  outliers final: 11
  residues processed: 79
  average time/residue: 0.0547
  time to fit residues: 5.8670
Evaluate side-chains
  70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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  150 SER
Chi-restraints excluded: chain A residue  206 LEU
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  303 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 48 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0060
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    1.0600

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.096712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.081074 restraints weight = 14819.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.083040 restraints weight = 8900.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.084361 restraints weight = 6306.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.085164 restraints weight = 4978.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.085851 restraints weight = 4247.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4270  Z= 0.110
  Angle     :  0.611   9.983   5792  Z= 0.283
  Chirality :  0.037   0.155    704
  Planarity :  0.004   0.035    712
  Dihedral  :  4.440  18.231    586
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 23.04 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.37), residues: 524
  helix:  1.83 (0.29), residues: 324
  sheet: -1.61 (0.71), residues: 56
  loop : -2.29 (0.44), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 315 
 TYR   0.015   0.001   TYR B 319 
 PHE   0.005   0.001   PHE B  95 
 TRP   0.007   0.001   TRP B 336 
 HIS   0.002   0.000   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 4270)
  covalent geometry    : angle       0.61062 ( 5792)
  hydrogen bonds       : bond        0.02947 (  252)
  hydrogen bonds       : angle       4.08702 (  750)

*********************** 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
  90 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7976 (mt) cc_final: 0.7621 (tp)
REVERT: A  143 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8116 (ptpt)
REVERT: A  159 ASN cc_start: 0.8292 (t0) cc_final: 0.7898 (t0)
REVERT: A  266 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8170 (m-10)
REVERT: B  105 LEU cc_start: 0.7986 (mt) cc_final: 0.7646 (tp)
  outliers start: 16
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0511
  time to fit residues: 5.9111
Evaluate side-chains
  69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
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  206 LEU
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  130 CYS
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 21 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0870
   chunk 24 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0770
   chunk 35 optimal weight:    0.6980
   overall best weight:    2.9720

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

Flipped N/Q/H residues before XYZ refinement:
B  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.095739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.079572 restraints weight = 15463.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.081586 restraints weight = 9141.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.082911 restraints weight = 6440.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.083797 restraints weight = 5105.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.084366 restraints weight = 4367.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4270  Z= 0.145
  Angle     :  0.635   9.248   5792  Z= 0.298
  Chirality :  0.038   0.136    704
  Planarity :  0.004   0.032    712
  Dihedral  :  4.509  17.502    586
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.65 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.38), residues: 524
  helix:  1.87 (0.29), residues: 324
  sheet: -1.64 (0.72), residues: 56
  loop : -2.16 (0.45), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.009   0.001   TYR A 314 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.017   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4270)
  covalent geometry    : angle       0.63475 ( 5792)
  hydrogen bonds       : bond        0.03070 (  252)
  hydrogen bonds       : angle       4.18235 (  750)

*********************** 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: 17
    poor density    : 62
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.7945 (mt) cc_final: 0.7570 (tp)
REVERT: A  159 ASN cc_start: 0.8380 (t0) cc_final: 0.7888 (t0)
REVERT: A  266 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8163 (m-10)
REVERT: B  105 LEU cc_start: 0.7950 (mt) cc_final: 0.7613 (tp)
  outliers start: 17
  outliers final: 13
  residues processed: 74
  average time/residue: 0.0527
  time to fit residues: 5.2673
Evaluate side-chains
  71 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  206 LEU
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   66 LEU
Chi-restraints excluded: chain B residue  134 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0060
   chunk 7 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.098332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.082881 restraints weight = 14656.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.084887 restraints weight = 8603.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.086209 restraints weight = 6042.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.087150 restraints weight = 4750.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.087649 restraints weight = 4002.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4270  Z= 0.105
  Angle     :  0.603   7.556   5792  Z= 0.280
  Chirality :  0.037   0.151    704
  Planarity :  0.003   0.033    712
  Dihedral  :  4.245  16.113    586
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.38), residues: 524
  helix:  1.84 (0.29), residues: 336
  sheet: -1.38 (0.74), residues: 56
  loop : -2.07 (0.48), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 315 
 TYR   0.015   0.001   TYR B 319 
 PHE   0.005   0.001   PHE A  95 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.003   0.000   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4270)
  covalent geometry    : angle       0.60316 ( 5792)
  hydrogen bonds       : bond        0.02540 (  252)
  hydrogen bonds       : angle       3.92282 (  750)

*********************** 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
  82 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8067 (mt) cc_final: 0.7724 (tp)
REVERT: A  159 ASN cc_start: 0.8380 (t0) cc_final: 0.7935 (t0)
REVERT: A  266 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7983 (m-10)
REVERT: A  276 MET cc_start: 0.7974 (tmm) cc_final: 0.7766 (tmm)
REVERT: B  105 LEU cc_start: 0.7970 (mt) cc_final: 0.7643 (tp)
  outliers start: 12
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0470
  time to fit residues: 5.0014
Evaluate side-chains
  68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
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  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 50 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 1 optimal weight:   30.0000
   chunk 16 optimal weight:    9.9990
   chunk 19 optimal weight:    0.4980
   chunk 11 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 38 optimal weight:    0.2980
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.098721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.082906 restraints weight = 14646.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.084882 restraints weight = 9054.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.086204 restraints weight = 6510.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.087075 restraints weight = 5171.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.087781 restraints weight = 4422.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4270  Z= 0.107
  Angle     :  0.620   8.369   5792  Z= 0.286
  Chirality :  0.037   0.151    704
  Planarity :  0.004   0.036    712
  Dihedral  :  4.213  15.640    586
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 28.11 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.38), residues: 524
  helix:  2.16 (0.29), residues: 326
  sheet: -1.77 (0.71), residues: 60
  loop : -2.01 (0.46), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 315 
 TYR   0.010   0.001   TYR B 314 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.008   0.001   TRP A  99 
 HIS   0.004   0.000   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 4270)
  covalent geometry    : angle       0.61956 ( 5792)
  hydrogen bonds       : bond        0.02536 (  252)
  hydrogen bonds       : angle       3.88588 (  750)

*********************** 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
  77 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  105 LEU cc_start: 0.8055 (mt) cc_final: 0.7704 (tp)
REVERT: A  159 ASN cc_start: 0.8376 (t0) cc_final: 0.7927 (t0)
REVERT: A  266 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7979 (m-10)
REVERT: B  105 LEU cc_start: 0.7975 (mt) cc_final: 0.7664 (tp)
REVERT: B  308 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8234 (mmtp)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 0.0527
  time to fit residues: 5.2918
Evaluate side-chains
  69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain B residue  148 GLU
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 31 optimal weight:    0.0270
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0770
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0030
   chunk 10 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    1.2210

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.098909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.083170 restraints weight = 14651.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.085170 restraints weight = 8929.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.086514 restraints weight = 6381.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.087490 restraints weight = 5053.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.088010 restraints weight = 4251.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4270  Z= 0.109
  Angle     :  0.630   8.221   5792  Z= 0.288
  Chirality :  0.038   0.171    704
  Planarity :  0.004   0.035    712
  Dihedral  :  4.191  19.744    586
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 27.88 %
    Favored  : 69.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.38), residues: 524
  helix:  2.25 (0.29), residues: 326
  sheet: -1.73 (0.72), residues: 60
  loop : -2.00 (0.47), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.029   0.002   TYR A 319 
 PHE   0.007   0.001   PHE A  95 
 TRP   0.005   0.001   TRP A  99 
 HIS   0.003   0.001   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4270)
  covalent geometry    : angle       0.62976 ( 5792)
  hydrogen bonds       : bond        0.02510 (  252)
  hydrogen bonds       : angle       3.88104 (  750)

*********************** 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
  74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LEU cc_start: 0.8061 (mt) cc_final: 0.7727 (tp)
REVERT: A  159 ASN cc_start: 0.8388 (t0) cc_final: 0.7941 (t0)
REVERT: A  266 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7946 (m-10)
REVERT: A  308 LYS cc_start: 0.7770 (mttt) cc_final: 0.7126 (tppt)
REVERT: B  105 LEU cc_start: 0.8035 (mt) cc_final: 0.7718 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0459
  time to fit residues: 4.6791
Evaluate side-chains
  70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  150 SER
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
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 0 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:    0.2980
   chunk 7 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    2.8384

-------------------------------------------------------------------------------
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 = 0.3576 r_free = 0.3576 target = 0.097237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.081301 restraints weight = 14545.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.083278 restraints weight = 8958.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.084657 restraints weight = 6409.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.085523 restraints weight = 5093.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.086215 restraints weight = 4348.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.4532

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= 0.139
  Angle     :  0.643   8.927   5792  Z= 0.297
  Chirality :  0.038   0.141    704
  Planarity :  0.004   0.038    712
  Dihedral  :  4.234  19.239    586
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 27.88 %
    Favored  : 69.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.38), residues: 524
  helix:  2.33 (0.29), residues: 326
  sheet: -1.82 (0.72), residues: 60
  loop : -2.10 (0.45), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 294 
 TYR   0.008   0.001   TYR A 314 
 PHE   0.015   0.002   PHE B  95 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.003   0.001   HIS B  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4270)
  covalent geometry    : angle       0.64344 ( 5792)
  hydrogen bonds       : bond        0.02791 (  252)
  hydrogen bonds       : angle       3.98715 (  750)

********************** 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
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  105 LEU cc_start: 0.8112 (mt) cc_final: 0.7759 (tp)
REVERT: A  159 ASN cc_start: 0.8404 (t0) cc_final: 0.7989 (t0)
REVERT: A  266 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8090 (m-10)
REVERT: A  319 TYR cc_start: 0.8983 (p90) cc_final: 0.8591 (p90)
REVERT: B   70 CYS cc_start: 0.8665 (m) cc_final: 0.8420 (t)
REVERT: B  105 LEU cc_start: 0.8108 (mt) cc_final: 0.7765 (tp)
REVERT: B  308 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8300 (mmtp)
  outliers start: 10
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0487
  time to fit residues: 4.6669
Evaluate side-chains
  68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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  150 SER
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  272 THR
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 27 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3521 r_free = 0.3521 target = 0.094593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.078653 restraints weight = 15414.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.080578 restraints weight = 9421.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.081894 restraints weight = 6801.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.082691 restraints weight = 5484.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.083434 restraints weight = 4761.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4270  Z= 0.207
  Angle     :  0.734  11.024   5792  Z= 0.343
  Chirality :  0.040   0.132    704
  Planarity :  0.004   0.037    712
  Dihedral  :  4.553  20.286    586
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 28.11 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.38), residues: 524
  helix:  2.09 (0.29), residues: 326
  sheet: -2.05 (0.70), residues: 60
  loop : -2.09 (0.47), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.016   0.002   TYR B 319 
 PHE   0.018   0.002   PHE B  95 
 TRP   0.011   0.002   TRP A 336 
 HIS   0.003   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 4270)
  covalent geometry    : angle       0.73359 ( 5792)
  hydrogen bonds       : bond        0.03471 (  252)
  hydrogen bonds       : angle       4.36733 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 757.14 seconds
wall clock time: 13 minutes 45.89 seconds (825.89 seconds total)