Starting phenix.real_space_refine
on Wed Mar 12 00:52:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xan_38202/03_2025/8xan_38202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xan_38202/03_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_38202/03_2025/8xan_38202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xan_38202/03_2025/8xan_38202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xan_38202/03_2025/8xan_38202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xan_38202/03_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-5624/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: 4.87, per 1000 atoms: 0.70
  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: 1.64
  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: 0.70
  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: 1.87

  Time building geometry restraints manager: 1.99 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:             0.960
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.020
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.350
-------------------------------------------------------------------------------
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  : 0.733 
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: 0.2027
  time to fit residues: 45.6694
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  : 0.802 
-------------------------------------------------------------------------------
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 = 0.116054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.106712 restraints weight = 12383.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.108999 restraints weight = 6912.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.110511 restraints weight = 4498.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
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  : 0.718 
Fit side-chains
   revert: symmetry clash
REVERT: B    3 ASP cc_start: 0.7750 (m-30) cc_final: 0.7530 (m-30)
REVERT: B   55 MET cc_start: 0.6683 (tpp) cc_final: 0.6379 (tpp)
REVERT: B  134 ILE cc_start: 0.8558 (mt) cc_final: 0.8231 (tt)
REVERT: B  258 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7652 (p0)
REVERT: A  297 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8178 (mm)
  outliers start: 12
  outliers final: 4
  residues processed: 105
  average time/residue: 0.1650
  time to fit residues: 24.2003
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  : 0.819 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 89 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.107130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.097776 restraints weight = 12842.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099948 restraints weight = 7293.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.101386 restraints weight = 4830.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4870

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     :  0.662   8.129   9624  Z= 0.347
  Chirality :  0.048   0.140   1134
  Planarity :  0.006   0.048   1245
  Dihedral  :  5.297  55.067    983
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.97 %
    Favored  : 81.38 %
  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: -1.81 (0.25), residues: 912
  helix:  0.14 (1.05), residues: 30
  sheet: -0.79 (0.27), residues: 342
  loop : -1.58 (0.23), residues: 540

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  : 0.916 
Fit side-chains
REVERT: B  134 ILE cc_start: 0.8580 (mt) cc_final: 0.8277 (tt)
REVERT: B  173 MET cc_start: 0.7900 (mmt) cc_final: 0.7646 (mmt)
REVERT: A   46 GLU cc_start: 0.5704 (pp20) cc_final: 0.5497 (pp20)
REVERT: A  297 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8230 (mm)
REVERT: C   52 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8487 (ptt90)
  outliers start: 28
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1938
  time to fit residues: 24.0342
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  : 0.782 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 87 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    2.7986

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.108622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.099450 restraints weight = 12820.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.101644 restraints weight = 7181.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.103101 restraints weight = 4694.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.4984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7089  Z= 0.215
  Angle     :  0.524   8.971   9624  Z= 0.273
  Chirality :  0.044   0.140   1134
  Planarity :  0.004   0.027   1245
  Dihedral  :  4.757  53.299    983
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.97 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.26), residues: 912
  helix:  0.47 (1.06), 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 B  89 
 HIS   0.005   0.001   HIS B 179 
 PHE   0.011   0.001   PHE A 176 
 TYR   0.021   0.001   TYR C  17 
 ARG   0.006   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
  74 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.724 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7705 (tp30) cc_final: 0.7448 (tp30)
REVERT: B  173 MET cc_start: 0.7853 (mmt) cc_final: 0.7559 (mmt)
REVERT: B  219 ARG cc_start: 0.8113 (ttp-170) cc_final: 0.7897 (ttp80)
REVERT: A  297 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8026 (mm)
  outliers start: 12
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1478
  time to fit residues: 15.6476
Evaluate side-chains
  67 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 68 optimal weight:    8.9990
   chunk 55 optimal weight:    0.2980
   chunk 26 optimal weight:    9.9990
   chunk 85 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    4.6588

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.102624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.093692 restraints weight = 13339.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095764 restraints weight = 7627.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.097158 restraints weight = 5044.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   7089  Z= 0.338
  Angle     :  0.604   7.952   9624  Z= 0.313
  Chirality :  0.047   0.146   1134
  Planarity :  0.005   0.035   1245
  Dihedral  :  5.184  47.786    983
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 16.54 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.84 (0.25), residues: 912
  helix:  0.26 (1.05), residues: 30
  sheet: -0.87 (0.26), residues: 351
  loop : -1.57 (0.23), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  89 
 HIS   0.005   0.001   HIS C   7 
 PHE   0.020   0.002   PHE B 176 
 TYR   0.012   0.002   TYR B 229 
 ARG   0.004   0.000   ARG B 219 

*********************** 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
  95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 67
  time to evaluate  : 0.896 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7788 (tp30) cc_final: 0.7525 (tp30)
REVERT: B  134 ILE cc_start: 0.8537 (mt) cc_final: 0.8236 (tt)
REVERT: B  173 MET cc_start: 0.7887 (mmt) cc_final: 0.7674 (mmt)
REVERT: A  114 SER cc_start: 0.8608 (p) cc_final: 0.8389 (t)
REVERT: A  215 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.6441 (mm110)
REVERT: A  297 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8061 (mm)
REVERT: C  187 ILE cc_start: 0.7425 (mm) cc_final: 0.7185 (mm)
  outliers start: 28
  outliers final: 21
  residues processed: 93
  average time/residue: 0.1541
  time to fit residues: 20.8853
Evaluate side-chains
  85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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 B residue  193 LEU
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  150 ASN
Chi-restraints excluded: chain A residue  215 GLN
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  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:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0020
   chunk 11 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    2.9996

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.103960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.095181 restraints weight = 13365.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.097258 restraints weight = 7613.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.098633 restraints weight = 4996.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7089  Z= 0.225
  Angle     :  0.529   8.625   9624  Z= 0.276
  Chirality :  0.045   0.161   1134
  Planarity :  0.004   0.031   1245
  Dihedral  :  4.814  44.839    983
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.36 %
    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: -1.48 (0.26), residues: 912
  helix:  0.52 (1.07), residues: 30
  sheet: -0.53 (0.26), residues: 405
  loop : -1.46 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  89 
 HIS   0.006   0.001   HIS B 179 
 PHE   0.011   0.001   PHE A 176 
 TYR   0.009   0.001   TYR C  17 
 ARG   0.004   0.000   ARG C  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
  92 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.698 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7574 (tp30) cc_final: 0.7332 (tp30)
REVERT: B  134 ILE cc_start: 0.8464 (mt) cc_final: 0.8122 (tt)
REVERT: B  173 MET cc_start: 0.7877 (mmt) cc_final: 0.7671 (mmt)
REVERT: B  268 LYS cc_start: 0.8607 (ptpt) cc_final: 0.8119 (mtpt)
REVERT: A  114 SER cc_start: 0.8589 (p) cc_final: 0.8388 (t)
REVERT: C  187 ILE cc_start: 0.7378 (mm) cc_final: 0.7171 (mm)
  outliers start: 24
  outliers final: 17
  residues processed: 90
  average time/residue: 0.1563
  time to fit residues: 20.4557
Evaluate side-chains
  78 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
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  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  150 ASN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain C residue   36 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    0.1980
   chunk 73 optimal weight:    8.9990
   chunk 80 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    2.5786

-------------------------------------------------------------------------------
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 = 0.3346 r_free = 0.3346 target = 0.104201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.095460 restraints weight = 13114.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.097559 restraints weight = 7408.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.098928 restraints weight = 4841.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.5557

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= 0.201
  Angle     :  0.519   8.546   9624  Z= 0.267
  Chirality :  0.044   0.139   1134
  Planarity :  0.004   0.030   1245
  Dihedral  :  4.620  43.195    983
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.88 %
    Favored  : 78.26 %
  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: -1.33 (0.27), residues: 912
  helix:  0.61 (1.08), residues: 30
  sheet: -0.41 (0.26), residues: 405
  loop : -1.38 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP B  89 
 HIS   0.007   0.001   HIS B 179 
 PHE   0.011   0.001   PHE B 176 
 TYR   0.019   0.001   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
  79 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.880 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7554 (tp30) cc_final: 0.7317 (tp30)
REVERT: B  134 ILE cc_start: 0.8441 (mt) cc_final: 0.8092 (tt)
REVERT: B  173 MET cc_start: 0.7845 (mmt) cc_final: 0.7615 (mmt)
REVERT: B  268 LYS cc_start: 0.8668 (ptpt) cc_final: 0.8176 (mtpt)
REVERT: A  114 SER cc_start: 0.8545 (p) cc_final: 0.8339 (t)
REVERT: C  187 ILE cc_start: 0.7353 (mm) cc_final: 0.7135 (mm)
  outliers start: 22
  outliers final: 20
  residues processed: 78
  average time/residue: 0.1725
  time to fit residues: 20.7172
Evaluate side-chains
  75 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
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  193 LEU
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue   57 ILE
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   34 THR
Chi-restraints excluded: chain C residue   36 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 43 optimal weight:    0.3980
   chunk 47 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0970
   chunk 13 optimal weight:    0.0870
   overall best weight:    2.1160

-------------------------------------------------------------------------------
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 = 0.3351 r_free = 0.3351 target = 0.104622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.095935 restraints weight = 13143.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.098039 restraints weight = 7375.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.099397 restraints weight = 4793.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.5616

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= 0.171
  Angle     :  0.492   8.352   9624  Z= 0.256
  Chirality :  0.043   0.134   1134
  Planarity :  0.004   0.029   1245
  Dihedral  :  4.465  42.628    983
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.36 %
    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: -1.22 (0.27), residues: 912
  helix:  0.72 (1.08), residues: 30
  sheet: -0.32 (0.26), residues: 405
  loop : -1.32 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B  89 
 HIS   0.007   0.001   HIS B 179 
 PHE   0.008   0.001   PHE A 176 
 TYR   0.024   0.001   TYR A  17 
 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
  87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 60
  time to evaluate  : 1.328 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7547 (tp30) cc_final: 0.7270 (tp30)
REVERT: B  134 ILE cc_start: 0.8409 (mt) cc_final: 0.8052 (tt)
REVERT: B  173 MET cc_start: 0.7833 (mmt) cc_final: 0.7597 (mmt)
REVERT: B  268 LYS cc_start: 0.8593 (ptpt) cc_final: 0.8109 (mtpt)
REVERT: A   46 GLU cc_start: 0.5584 (pp20) cc_final: 0.4594 (mm-30)
REVERT: A  114 SER cc_start: 0.8528 (p) cc_final: 0.8317 (t)
REVERT: A  273 GLN cc_start: 0.7571 (tt0) cc_final: 0.7225 (tt0)
REVERT: C   84 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7998 (tt)
REVERT: C  187 ILE cc_start: 0.7330 (mm) cc_final: 0.7106 (mm)
  outliers start: 27
  outliers final: 20
  residues processed: 85
  average time/residue: 0.1615
  time to fit residues: 21.2167
Evaluate side-chains
  78 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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  113 THR
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   34 THR
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 61 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 75 optimal weight:    0.1980
   chunk 17 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 79 optimal weight:    0.5980
   overall best weight:    2.5384

-------------------------------------------------------------------------------
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 = 0.104124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.095326 restraints weight = 13260.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.097445 restraints weight = 7422.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.098818 restraints weight = 4828.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.5696

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= 0.197
  Angle     :  0.517   8.878   9624  Z= 0.265
  Chirality :  0.044   0.178   1134
  Planarity :  0.004   0.029   1245
  Dihedral  :  4.484  40.935    983
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.36 %
    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: -1.19 (0.27), residues: 912
  helix:  0.70 (1.07), residues: 30
  sheet: -0.29 (0.26), residues: 405
  loop : -1.31 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP B  89 
 HIS   0.003   0.001   HIS C   7 
 PHE   0.011   0.001   PHE B 176 
 TYR   0.023   0.001   TYR A  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: 25
    poor density    : 60
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLU cc_start: 0.7507 (tp30) cc_final: 0.7285 (tp30)
REVERT: B  134 ILE cc_start: 0.8414 (mt) cc_final: 0.8062 (tt)
REVERT: B  173 MET cc_start: 0.7844 (mmt) cc_final: 0.7596 (mmt)
REVERT: B  268 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8125 (mtpt)
REVERT: A  114 SER cc_start: 0.8539 (p) cc_final: 0.8332 (t)
REVERT: A  275 ASP cc_start: 0.7134 (m-30) cc_final: 0.6833 (m-30)
REVERT: C  157 THR cc_start: 0.7978 (m) cc_final: 0.7696 (p)
REVERT: C  187 ILE cc_start: 0.7318 (mm) cc_final: 0.7089 (mm)
  outliers start: 25
  outliers final: 23
  residues processed: 84
  average time/residue: 0.1357
  time to fit residues: 17.3447
Evaluate side-chains
  81 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
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  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   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   34 THR
Chi-restraints excluded: chain C residue   36 LEU
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:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0270
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   overall best weight:    5.1844

-------------------------------------------------------------------------------
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 = 0.3274 r_free = 0.3274 target = 0.099883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.090949 restraints weight = 13317.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.093017 restraints weight = 7591.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.094436 restraints weight = 5007.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   7089  Z= 0.373
  Angle     :  0.610   7.481   9624  Z= 0.317
  Chirality :  0.047   0.166   1134
  Planarity :  0.005   0.034   1245
  Dihedral  :  5.234  55.665    983
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 18.49 %
    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: -1.46 (0.26), residues: 912
  helix:  0.32 (1.07), residues: 30
  sheet: -0.45 (0.26), residues: 405
  loop : -1.51 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  89 
 HIS   0.005   0.001   HIS A   7 
 PHE   0.021   0.002   PHE A 176 
 TYR   0.023   0.002   TYR A  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
  82 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLU cc_start: 0.7659 (tp30) cc_final: 0.7395 (tp30)
REVERT: B  134 ILE cc_start: 0.8506 (mt) cc_final: 0.8226 (tt)
REVERT: B  173 MET cc_start: 0.7936 (mmt) cc_final: 0.7628 (mmt)
REVERT: C  157 THR cc_start: 0.8100 (m) cc_final: 0.7813 (p)
  outliers start: 23
  outliers final: 21
  residues processed: 79
  average time/residue: 0.1333
  time to fit residues: 16.2680
Evaluate side-chains
  78 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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  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  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   34 THR
Chi-restraints excluded: chain C residue   36 LEU
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 10 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0040
   chunk 15 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    2.0998

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.102687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.093778 restraints weight = 13371.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.095830 restraints weight = 7626.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.097209 restraints weight = 5007.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.5846

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= 0.169
  Angle     :  0.512   9.264   9624  Z= 0.261
  Chirality :  0.044   0.178   1134
  Planarity :  0.004   0.028   1245
  Dihedral  :  4.561  49.079    983
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.27 %
    Favored  : 77.99 %
  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: -1.21 (0.27), residues: 912
  helix:  0.67 (1.08), residues: 30
  sheet: -0.18 (0.27), residues: 396
  loop : -1.45 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  89 
 HIS   0.002   0.001   HIS A   7 
 PHE   0.008   0.001   PHE C  74 
 TYR   0.023   0.001   TYR A  17 
 ARG   0.003   0.000   ARG A  52 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1889.52 seconds
wall clock time: 33 minutes 48.26 seconds (2028.26 seconds total)