Starting phenix.real_space_refine
on Tue Jan 14 16:36:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xan_38202/01_2025/8xan_38202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xan_38202/01_2025/8xan_38202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xan_38202/01_2025/8xan_38202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xan_38202/01_2025/8xan_38202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xan_38202/01_2025/8xan_38202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xan_38202/01_2025/8xan_38202.cif"
  }
  resolution = 3.5
  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=   0.007
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      30      5.16       5
     C    4383      2.51       5
     N    1164      2.21       5
     O    1386      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6963
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2321
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 14, 'TRANS': 291}
    Chain: "A"
      Number of atoms: 2321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2321
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 14, 'TRANS': 291}
    Chain: "C"
      Number of atoms: 2321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2321
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 14, 'TRANS': 291}
  Time building chain proxies: 4.44, per 1000 atoms: 0.64
  Number of scatterers: 6963
  At special positions: 0
  Unit cell: (105.6, 108.24, 63.36, 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      30     16.00
     O    1386      8.00
     N    1164      7.00
     C    4383      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 6 sheets defined
      6.8% alpha, 24.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'B' and resid 77 through 86
    Processing helix  chain 'B' and resid 113 through 117
    Processing helix  chain 'A' and resid 77 through 86
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 4.399A  pdb=" N   LYS A 238 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   PHE A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 234 through 239'
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 3.571A  pdb=" N   ILE A 296 " --> pdb=" O   ASP A 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 86
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'C' and resid 234 through 239
      removed outlier: 4.416A  pdb=" N   LYS C 238 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   PHE C 239 " --> pdb=" O   LEU C 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 234 through 239'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 13
      removed outlier: 5.671A  pdb=" N   LEU B  13 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ALA B  25 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 25 through 28
    current: chain 'B' and resid 57 through 71
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 57 through 71
    current: chain 'B' and resid 119 through 135
      removed outlier: 6.531A  pdb=" N   GLY B 145 " --> pdb=" O   ASN B 128 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   MET B 130 " --> pdb=" O   THR B 143 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   THR B 143 " --> pdb=" O   MET B 130 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LEU B 132 " --> pdb=" O   MET B 141 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   MET B 141 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE B 134 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
      removed outlier: 8.624A  pdb=" N   ILE B 139 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 138 through 148
    current: chain 'B' and resid 221 through 229
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 221 through 229
    current: chain 'B' and resid 259 through 269
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 204
      removed outlier: 4.120A  pdb=" N   LYS B 214 " --> pdb=" O   ARG B 204 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 13
      removed outlier: 5.638A  pdb=" N   LEU A  13 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ALA A  25 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 25 through 28
    current: chain 'A' and resid 57 through 71
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 57 through 71
    current: chain 'A' and resid 119 through 135
      removed outlier: 6.477A  pdb=" N   GLY A 145 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   MET A 130 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   THR A 143 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   LEU A 132 " --> pdb=" O   MET A 141 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   MET A 141 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ILE A 134 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   ILE A 139 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 138 through 148
    current: chain 'A' and resid 221 through 229
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 221 through 229
    current: chain 'A' and resid 262 through 269
    Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204
      removed outlier: 3.972A  pdb=" N   LYS A 214 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 13
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 27 through 28
    current: chain 'C' and resid 57 through 71
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 57 through 71
    current: chain 'C' and resid 119 through 135
      removed outlier: 6.342A  pdb=" N   GLY C 145 " --> pdb=" O   ASN C 128 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   MET C 130 " --> pdb=" O   THR C 143 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   THR C 143 " --> pdb=" O   MET C 130 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LEU C 132 " --> pdb=" O   MET C 141 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   MET C 141 " --> pdb=" O   LEU C 132 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE C 134 " --> pdb=" O   ILE C 139 " (cutoff:3.500A)
      removed outlier: 8.487A  pdb=" N   ILE C 139 " --> pdb=" O   ILE C 134 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 138 through 148
    current: chain 'C' and resid 221 through 229
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 221 through 229
    current: chain 'C' and resid 260 through 269
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 260 through 269
    current: chain 'C' and resid 283 through 290
    Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 204
      removed outlier: 4.119A  pdb=" N   LYS C 214 " --> pdb=" O   ARG C 204 " (cutoff:3.500A)

    53 hydrogen bonds defined for protein.
    126 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: 1.51

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1644
        1.33 -     1.45: 1367
        1.45 -     1.57: 4021
        1.57 -     1.69: 3
        1.69 -     1.81: 54
  Bond restraints: 7089
  Sorted by residual:
  bond pdb=" N   GLY C  87 "
       pdb=" CA  GLY C  87 "
    ideal  model  delta    sigma   weight residual
    1.442  1.476 -0.034 7.70e-03 1.69e+04 1.95e+01
  bond pdb=" N   GLY A  97 "
       pdb=" CA  GLY A  97 "
    ideal  model  delta    sigma   weight residual
    1.445  1.477 -0.032 8.30e-03 1.45e+04 1.48e+01
  bond pdb=" N   GLY B  87 "
       pdb=" CA  GLY B  87 "
    ideal  model  delta    sigma   weight residual
    1.445  1.476 -0.032 9.20e-03 1.18e+04 1.18e+01
  bond pdb=" N   ILE A  57 "
       pdb=" CA  ILE A  57 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.11e-02 8.12e+03 1.17e+01
  bond pdb=" N   ILE A 146 "
       pdb=" CA  ILE A 146 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.15e-02 7.56e+03 1.16e+01
  ... (remaining 7084 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 6587
        1.08 -     2.16: 2127
        2.16 -     3.25: 772
        3.25 -     4.33: 125
        4.33 -     5.41: 13
  Bond angle restraints: 9624
  Sorted by residual:
  angle pdb=" CA  GLY C  56 "
        pdb=" C   GLY C  56 "
        pdb=" O   GLY C  56 "
      ideal   model   delta    sigma   weight residual
     122.22  118.13    4.09 6.50e-01 2.37e+00 3.95e+01
  angle pdb=" CA  GLY A  56 "
        pdb=" C   GLY A  56 "
        pdb=" O   GLY A  56 "
      ideal   model   delta    sigma   weight residual
     122.13  118.14    3.99 8.90e-01 1.26e+00 2.01e+01
  angle pdb=" N   ILE B 296 "
        pdb=" CA  ILE B 296 "
        pdb=" C   ILE B 296 "
      ideal   model   delta    sigma   weight residual
     112.83  108.45    4.38 9.90e-01 1.02e+00 1.95e+01
  angle pdb=" CA  GLY B  87 "
        pdb=" C   GLY B  87 "
        pdb=" O   GLY B  87 "
      ideal   model   delta    sigma   weight residual
     122.33  117.90    4.43 1.11e+00 8.12e-01 1.59e+01
  angle pdb=" N   ASP B  51 "
        pdb=" CA  ASP B  51 "
        pdb=" C   ASP B  51 "
      ideal   model   delta    sigma   weight residual
     113.20  108.45    4.75 1.21e+00 6.83e-01 1.54e+01
  ... (remaining 9619 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.96: 3725
       14.96 -    29.92: 372
       29.92 -    44.88: 94
       44.88 -    59.84: 32
       59.84 -    74.80: 25
  Dihedral angle restraints: 4248
    sinusoidal: 1641
      harmonic: 2607
  Sorted by residual:
  dihedral pdb=" CD  ARG A 219 "
           pdb=" NE  ARG A 219 "
           pdb=" CZ  ARG A 219 "
           pdb=" NH1 ARG A 219 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   35.11  -35.11     1      1.00e+01 1.00e-02 1.75e+01
  dihedral pdb=" CD  ARG A  49 "
           pdb=" NE  ARG A  49 "
           pdb=" CZ  ARG A  49 "
           pdb=" NH1 ARG A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   29.73  -29.73     1      1.00e+01 1.00e-02 1.26e+01
  dihedral pdb=" CD  ARG C 101 "
           pdb=" NE  ARG C 101 "
           pdb=" CZ  ARG C 101 "
           pdb=" NH1 ARG C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   27.23  -27.23     1      1.00e+01 1.00e-02 1.06e+01
  ... (remaining 4245 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 524
       0.044 -    0.088: 252
       0.088 -    0.132: 224
       0.132 -    0.176: 95
       0.176 -    0.219: 39
  Chirality restraints: 1134
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  ILE A  29 "
            pdb=" N   ILE A  29 "
            pdb=" C   ILE A  29 "
            pdb=" CB  ILE A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  ILE A 267 "
            pdb=" N   ILE A 267 "
            pdb=" C   ILE A 267 "
            pdb=" CB  ILE A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 1131 not shown)

  Planarity restraints: 1245
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 219 "   -0.635 9.50e-02 1.11e+02   2.85e-01 4.94e+01
        pdb=" NE  ARG A 219 "    0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 219 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 219 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 219 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  49 "   -0.526 9.50e-02 1.11e+02   2.36e-01 3.41e+01
        pdb=" NE  ARG A  49 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  49 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  49 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  49 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 101 "   -0.483 9.50e-02 1.11e+02   2.16e-01 2.87e+01
        pdb=" NE  ARG C 101 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 101 "    0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 101 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 101 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1242 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1896
        2.82 -     3.34: 6313
        3.34 -     3.86: 12208
        3.86 -     4.38: 14060
        4.38 -     4.90: 23246
  Nonbonded interactions: 57723
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  78 "
            pdb=" OH  TYR C 260 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" N   LEU C  43 "
            pdb=" O   ARG C  58 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" N   LEU B  43 "
            pdb=" O   ARG B  58 "
     model   vdw
     2.403 3.120
  nonbonded pdb=" N   LEU A  43 "
            pdb=" O   ARG A  58 "
     model   vdw
     2.403 3.120
  nonbonded pdb=" OE2 GLU B  14 "
            pdb=" OG  SER B 104 "
     model   vdw
     2.419 3.040
  ... (remaining 57718 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'
  selection = chain 'C'
}

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:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.450
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
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      :  0.011   0.083   7089  Z= 0.718
  Angle     :  1.186   5.409   9624  Z= 0.899
  Chirality :  0.082   0.219   1134
  Planarity :  0.021   0.285   1245
  Dihedral  : 14.665  74.798   2580
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 11.72 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.25), residues: 912
  helix: -2.00 (0.70), residues: 48
  sheet: -0.79 (0.26), residues: 372
  loop : -1.99 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  89 
 HIS   0.005   0.001   HIS C   7 
 PHE   0.015   0.001   PHE A 109 
 TYR   0.008   0.001   TYR C  17 
 ARG   0.005   0.001   ARG A 101 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: B  171 GLU cc_start: 0.5991 (tt0) cc_final: 0.5508 (pt0)
REVERT: B  176 PHE cc_start: 0.4933 (m-10) cc_final: 0.4214 (m-10)
REVERT: A   53 ASN cc_start: 0.6745 (m-40) cc_final: 0.6492 (m-40)
REVERT: A  285 SER cc_start: 0.8697 (t) cc_final: 0.8342 (p)
REVERT: C   46 GLU cc_start: 0.8133 (tp30) cc_final: 0.6975 (pp20)
REVERT: C   63 GLN cc_start: 0.6534 (pt0) cc_final: 0.6278 (tt0)
REVERT: C  186 ASP cc_start: 0.6297 (t0) cc_final: 0.6090 (t0)
REVERT: C  293 ASP cc_start: 0.8234 (t70) cc_final: 0.7994 (t0)
  outliers start: 12
  outliers final: 4
  residues processed: 172
  average time/residue: 0.2034
  time to fit residues: 45.8851
Evaluate side-chains
  115 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  187 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
B  63 GLN
B 179 HIS
C 110 ASN
C 273 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.116053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.106728 restraints weight = 12383.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.109010 restraints weight = 6919.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.110524 restraints weight = 4506.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7089  Z= 0.297
  Angle     :  0.654   9.288   9624  Z= 0.344
  Chirality :  0.048   0.146   1134
  Planarity :  0.005   0.050   1245
  Dihedral  :  4.904  52.784    989
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.45 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.26), residues: 912
  helix:  0.11 (1.07), residues: 30
  sheet: -0.70 (0.25), residues: 399
  loop : -1.49 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  89 
 HIS   0.006   0.002   HIS A   7 
 PHE   0.024   0.002   PHE B 230 
 TYR   0.014   0.002   TYR B 260 
 ARG   0.006   0.001   ARG B   6 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: B    3 ASP cc_start: 0.7749 (m-30) cc_final: 0.7529 (m-30)
REVERT: B   55 MET cc_start: 0.6680 (tpp) cc_final: 0.6377 (tpp)
REVERT: B  134 ILE cc_start: 0.8558 (mt) cc_final: 0.8232 (tt)
REVERT: B  258 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7653 (p0)
REVERT: A  297 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8178 (mm)
  outliers start: 12
  outliers final: 4
  residues processed: 105
  average time/residue: 0.1709
  time to fit residues: 24.9850
Evaluate side-chains
  72 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain C residue   36 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 89 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
B  63 GLN
A  96 ASN
A 215 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.107147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.097787 restraints weight = 12844.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099975 restraints weight = 7276.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.101415 restraints weight = 4813.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   7089  Z= 0.397
  Angle     :  0.661   8.098   9624  Z= 0.347
  Chirality :  0.048   0.150   1134
  Planarity :  0.006   0.048   1245
  Dihedral  :  5.292  54.831    983
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.84 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.25), residues: 912
  helix:  0.12 (1.04), residues: 30
  sheet: -0.92 (0.26), residues: 354
  loop : -1.55 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  89 
 HIS   0.008   0.002   HIS C   7 
 PHE   0.027   0.003   PHE B 176 
 TYR   0.013   0.002   TYR C 229 
 ARG   0.005   0.001   ARG B 219 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 66
  time to evaluate  : 1.038 
Fit side-chains
REVERT: B  134 ILE cc_start: 0.8579 (mt) cc_final: 0.8277 (tt)
REVERT: B  173 MET cc_start: 0.7897 (mmt) cc_final: 0.7634 (mmt)
REVERT: A   46 GLU cc_start: 0.5697 (pp20) cc_final: 0.5495 (pp20)
REVERT: A  297 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8224 (mm)
REVERT: C   52 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8483 (ptt90)
  outliers start: 28
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1763
  time to fit residues: 22.0442
Evaluate side-chains
  77 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  151 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
C  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.105681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.096554 restraints weight = 13401.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098663 restraints weight = 7650.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.100094 restraints weight = 5070.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.5018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7089  Z= 0.219
  Angle     :  0.521   9.062   9624  Z= 0.271
  Chirality :  0.045   0.142   1134
  Planarity :  0.004   0.028   1245
  Dihedral  :  4.722  53.015    983
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.71 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.26), residues: 912
  helix:  0.46 (1.05), residues: 30
  sheet: -0.47 (0.25), residues: 405
  loop : -1.43 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  89 
 HIS   0.005   0.001   HIS B 179 
 PHE   0.011   0.002   PHE A 176 
 TYR   0.021   0.001   TYR C  17 
 ARG   0.005   0.000   ARG A  52 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.798 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7714 (tp30) cc_final: 0.7452 (tp30)
REVERT: B  146 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8722 (pt)
REVERT: B  173 MET cc_start: 0.7863 (mmt) cc_final: 0.7573 (mmt)
REVERT: B  219 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7875 (ttp80)
REVERT: A   75 GLU cc_start: 0.7391 (tp30) cc_final: 0.7186 (tp30)
REVERT: A  297 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8003 (mm)
  outliers start: 13
  outliers final: 8
  residues processed: 77
  average time/residue: 0.1677
  time to fit residues: 18.3922
Evaluate side-chains
  71 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 68 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0980
   chunk 26 optimal weight:    9.9990
   chunk 85 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   overall best weight:    3.3784

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.104020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.095039 restraints weight = 13305.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.097137 restraints weight = 7581.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.098507 restraints weight = 5008.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.5264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   7089  Z= 0.253
  Angle     :  0.549   8.345   9624  Z= 0.284
  Chirality :  0.045   0.150   1134
  Planarity :  0.004   0.030   1245
  Dihedral  :  4.817  49.910    983
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.41 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.25), residues: 912
  helix:  0.44 (1.06), residues: 30
  sheet: -0.76 (0.27), residues: 351
  loop : -1.47 (0.23), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  89 
 HIS   0.004   0.001   HIS C   7 
 PHE   0.015   0.002   PHE A 176 
 TYR   0.016   0.001   TYR C  17 
 ARG   0.003   0.000   ARG A  52 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.746 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7774 (tp30) cc_final: 0.7498 (tp30)
REVERT: B  134 ILE cc_start: 0.8443 (mt) cc_final: 0.8130 (tt)
REVERT: B  173 MET cc_start: 0.7860 (mmt) cc_final: 0.7617 (mmt)
REVERT: A  297 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7978 (mm)
REVERT: C   17 TYR cc_start: 0.8364 (t80) cc_final: 0.7760 (t80)
REVERT: C   52 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8501 (ptm-80)
  outliers start: 25
  outliers final: 19
  residues processed: 87
  average time/residue: 0.1521
  time to fit residues: 19.4528
Evaluate side-chains
  83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  285 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.099779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.090828 restraints weight = 13355.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.092934 restraints weight = 7565.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.094342 restraints weight = 4943.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.5629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   7089  Z= 0.402
  Angle     :  0.636   7.826   9624  Z= 0.332
  Chirality :  0.047   0.137   1134
  Planarity :  0.005   0.041   1245
  Dihedral  :  5.415  45.280    983
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 16.93 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.26), residues: 912
  helix:  0.08 (1.04), residues: 30
  sheet: -0.67 (0.25), residues: 405
  loop : -1.61 (0.24), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  89 
 HIS   0.009   0.002   HIS B 179 
 PHE   0.023   0.002   PHE B 176 
 TYR   0.015   0.002   TYR B 229 
 ARG   0.006   0.000   ARG A  52 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 68
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLU cc_start: 0.7749 (tp30) cc_final: 0.7515 (tp30)
REVERT: B  134 ILE cc_start: 0.8547 (mt) cc_final: 0.8273 (tt)
REVERT: C   30 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8066 (mtp180)
REVERT: C   52 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8577 (ptm-80)
REVERT: C  157 THR cc_start: 0.8215 (m) cc_final: 0.7846 (p)
REVERT: C  187 ILE cc_start: 0.7367 (mm) cc_final: 0.7133 (mm)
  outliers start: 35
  outliers final: 27
  residues processed: 101
  average time/residue: 0.1614
  time to fit residues: 23.6347
Evaluate side-chains
  87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 58
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  151 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain C residue   30 ARG
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  285 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 73 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   overall best weight:    3.7586

-------------------------------------------------------------------------------
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 = 0.3313 r_free = 0.3313 target = 0.102206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.093502 restraints weight = 13209.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.095558 restraints weight = 7486.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.096922 restraints weight = 4918.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.5698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7089  Z= 0.276
  Angle     :  0.559   8.266   9624  Z= 0.291
  Chirality :  0.045   0.164   1134
  Planarity :  0.004   0.030   1245
  Dihedral  :  5.129  49.925    983
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 17.97 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.26), residues: 912
  helix:  0.40 (1.07), residues: 30
  sheet: -0.63 (0.26), residues: 405
  loop : -1.57 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  89 
 HIS   0.007   0.001   HIS B 179 
 PHE   0.014   0.002   PHE B 176 
 TYR   0.020   0.002   TYR A  17 
 ARG   0.004   0.000   ARG A  52 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 60
  time to evaluate  : 0.833 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7735 (tp30) cc_final: 0.7483 (tp30)
REVERT: B  134 ILE cc_start: 0.8496 (mt) cc_final: 0.8215 (tt)
REVERT: B  268 LYS cc_start: 0.8588 (ptpt) cc_final: 0.8089 (mtpt)
REVERT: C   30 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8058 (mtp180)
REVERT: C   52 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8490 (ptm-80)
REVERT: C  157 THR cc_start: 0.8077 (m) cc_final: 0.7771 (p)
REVERT: C  187 ILE cc_start: 0.7316 (mm) cc_final: 0.7091 (mm)
  outliers start: 28
  outliers final: 23
  residues processed: 87
  average time/residue: 0.1567
  time to fit residues: 19.5914
Evaluate side-chains
  83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 58
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain C residue   30 ARG
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  285 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 179 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.102458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.093794 restraints weight = 13225.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.095819 restraints weight = 7467.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.097210 restraints weight = 4899.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7089  Z= 0.252
  Angle     :  0.553   8.411   9624  Z= 0.285
  Chirality :  0.045   0.144   1134
  Planarity :  0.004   0.031   1245
  Dihedral  :  4.997  56.157    983
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.62 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.26), residues: 912
  helix:  0.45 (1.07), residues: 30
  sheet: -0.56 (0.26), residues: 405
  loop : -1.52 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  89 
 HIS   0.007   0.001   HIS B 179 
 PHE   0.014   0.002   PHE B 176 
 TYR   0.009   0.001   TYR B 229 
 ARG   0.004   0.000   ARG A  52 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 64
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLU cc_start: 0.7673 (tp30) cc_final: 0.7467 (tp30)
REVERT: B  134 ILE cc_start: 0.8472 (mt) cc_final: 0.8186 (tt)
REVERT: B  268 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8096 (mtpt)
REVERT: A  284 LEU cc_start: 0.8114 (tp) cc_final: 0.7895 (tp)
REVERT: C   30 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8045 (mtp180)
REVERT: C   52 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8442 (ptm-80)
REVERT: C  157 THR cc_start: 0.8038 (m) cc_final: 0.7743 (p)
REVERT: C  187 ILE cc_start: 0.7104 (mm) cc_final: 0.6901 (mm)
  outliers start: 27
  outliers final: 23
  residues processed: 90
  average time/residue: 0.1693
  time to fit residues: 21.6477
Evaluate side-chains
  85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain C residue   30 ARG
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  285 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3320 r_free = 0.3320 target = 0.102650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.093902 restraints weight = 13352.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.095984 restraints weight = 7493.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.097325 restraints weight = 4874.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.5833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7089  Z= 0.241
  Angle     :  0.546   8.311   9624  Z= 0.283
  Chirality :  0.045   0.183   1134
  Planarity :  0.004   0.030   1245
  Dihedral  :  4.644  33.055    983
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.75 %
    Favored  : 78.12 %
  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: -1.47 (0.27), residues: 912
  helix:  0.48 (1.07), residues: 30
  sheet: -0.51 (0.26), residues: 405
  loop : -1.48 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  89 
 HIS   0.003   0.001   HIS A   7 
 PHE   0.013   0.001   PHE B 176 
 TYR   0.021   0.002   TYR C  17 
 ARG   0.003   0.000   ARG A  52 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLU cc_start: 0.7678 (tp30) cc_final: 0.7453 (tp30)
REVERT: B  134 ILE cc_start: 0.8459 (mt) cc_final: 0.8164 (tt)
REVERT: B  268 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8096 (mtpt)
REVERT: A  284 LEU cc_start: 0.8082 (tp) cc_final: 0.7857 (tp)
REVERT: C   17 TYR cc_start: 0.8326 (t80) cc_final: 0.7806 (t80)
REVERT: C   30 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8075 (mtp180)
REVERT: C   52 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8413 (ptm-80)
REVERT: C  157 THR cc_start: 0.8032 (m) cc_final: 0.7739 (p)
  outliers start: 24
  outliers final: 22
  residues processed: 84
  average time/residue: 0.1646
  time to fit residues: 19.7596
Evaluate side-chains
  82 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain C residue   30 ARG
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  285 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 179 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.099224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.090261 restraints weight = 13396.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.092336 restraints weight = 7610.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.093745 restraints weight = 4987.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.5977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   7089  Z= 0.383
  Angle     :  0.639   9.123   9624  Z= 0.329
  Chirality :  0.047   0.166   1134
  Planarity :  0.005   0.034   1245
  Dihedral  :  4.997  15.797    981
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.49 %
    Favored  : 78.12 %
  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: -1.65 (0.26), residues: 912
  helix:  0.18 (1.05), residues: 30
  sheet: -0.62 (0.26), residues: 405
  loop : -1.60 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  89 
 HIS   0.006   0.001   HIS A   7 
 PHE   0.018   0.002   PHE B 176 
 TYR   0.021   0.002   TYR C  17 
 ARG   0.004   0.001   ARG B 219 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 60
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLU cc_start: 0.7612 (tp30) cc_final: 0.7391 (tp30)
REVERT: B  134 ILE cc_start: 0.8508 (mt) cc_final: 0.8251 (tt)
REVERT: A  273 GLN cc_start: 0.7686 (tt0) cc_final: 0.7344 (tt0)
REVERT: A  275 ASP cc_start: 0.7337 (m-30) cc_final: 0.6940 (m-30)
REVERT: C   17 TYR cc_start: 0.8322 (t80) cc_final: 0.7771 (t80)
REVERT: C   30 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8118 (mtp180)
REVERT: C   52 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8315 (ptm-80)
REVERT: C  157 THR cc_start: 0.8152 (m) cc_final: 0.7871 (p)
  outliers start: 26
  outliers final: 22
  residues processed: 84
  average time/residue: 0.1584
  time to fit residues: 19.0061
Evaluate side-chains
  85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain C residue   30 ARG
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  285 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 83 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0030
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.0392

-------------------------------------------------------------------------------
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 = 0.3335 r_free = 0.3335 target = 0.103388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094465 restraints weight = 13360.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.096536 restraints weight = 7545.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.097858 restraints weight = 4941.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.5878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7089  Z= 0.117
  Angle     :  0.492   8.987   9624  Z= 0.255
  Chirality :  0.043   0.181   1134
  Planarity :  0.004   0.028   1245
  Dihedral  :  4.166  14.745    981
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.31 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.27), residues: 912
  helix:  0.72 (1.08), residues: 30
  sheet: -0.36 (0.26), residues: 405
  loop : -1.35 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B  89 
 HIS   0.002   0.000   HIS A 179 
 PHE   0.007   0.001   PHE C  74 
 TYR   0.019   0.001   TYR C  17 
 ARG   0.004   0.000   ARG A  52 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1805.40 seconds
wall clock time: 33 minutes 44.19 seconds (2024.19 seconds total)