Starting phenix.real_space_refine
on Fri Aug 22 18:44:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xan_38202/08_2025/8xan_38202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xan_38202/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xan_38202/08_2025/8xan_38202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xan_38202/08_2025/8xan_38202.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xan_38202/08_2025/8xan_38202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xan_38202/08_2025/8xan_38202.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.90, per 1000 atoms: 0.27
  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: 0.46
  Conformation dependent library (CDL) restraints added in 353.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.13
  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: 0.70

  Time building geometry restraints manager: 0.68 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: 0.01
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:             0.540
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.970
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.720
-------------------------------------------------------------------------------
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= 0.811
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.001   ARG A 101 
 TYR   0.008   0.001   TYR C  17 
 PHE   0.015   0.001   PHE A 109 
 TRP   0.004   0.001   TRP B  89 
 HIS   0.005   0.001   HIS C   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.01069 ( 7089)
  covalent geometry    : angle       1.18592 ( 9624)
  hydrogen bonds       : bond        0.19590 (   53)
  hydrogen bonds       : angle      10.28987 (  126)

*********************** 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  : 0.252 
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: 0.0744
  time to fit residues: 16.8474
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  : 0.228 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.7188

-------------------------------------------------------------------------------
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
A  96 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 = 0.3588 r_free = 0.3588 target = 0.119687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.110051 restraints weight = 12558.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.112422 restraints weight = 7025.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.113972 restraints weight = 4557.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.115040 restraints weight = 3273.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.115742 restraints weight = 2520.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3191

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= 0.170
  Angle     :  0.592  10.242   9624  Z= 0.312
  Chirality :  0.045   0.136   1134
  Planarity :  0.004   0.046   1245
  Dihedral  :  4.499  52.619    989
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.93 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.26), residues: 912
  helix: -1.41 (0.77), residues: 48
  sheet: -0.66 (0.26), residues: 399
  loop : -1.35 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 101 
 TYR   0.011   0.002   TYR A  17 
 PHE   0.028   0.002   PHE B 230 
 TRP   0.005   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7089)
  covalent geometry    : angle       0.59213 ( 9624)
  hydrogen bonds       : bond        0.02959 (   53)
  hydrogen bonds       : angle       6.29499 (  126)

*********************** 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
  105 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.173 
Fit side-chains
REVERT: B   55 MET cc_start: 0.6492 (tpp) cc_final: 0.6161 (tpp)
REVERT: B  134 ILE cc_start: 0.8568 (mt) cc_final: 0.8186 (tt)
REVERT: B  261 LYS cc_start: 0.8685 (tttt) cc_final: 0.8289 (tttm)
REVERT: A  297 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8095 (mm)
  outliers start: 13
  outliers final: 3
  residues processed: 102
  average time/residue: 0.0643
  time to fit residues: 9.2045
Evaluate side-chains
  70 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
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 29 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  63 GLN
B 128 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.096814 restraints weight = 12796.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.098940 restraints weight = 7307.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.100357 restraints weight = 4846.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.101351 restraints weight = 3555.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.102036 restraints weight = 2788.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.043   7089  Z= 0.317
  Angle     :  0.736   7.570   9624  Z= 0.388
  Chirality :  0.050   0.152   1134
  Planarity :  0.006   0.057   1245
  Dihedral  :  5.564  53.038    983
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.76 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.25), residues: 912
  helix:  0.01 (1.04), residues: 30
  sheet: -0.98 (0.26), residues: 354
  loop : -1.62 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 219 
 TYR   0.016   0.002   TYR C 229 
 PHE   0.032   0.003   PHE B 176 
 TRP   0.004   0.002   TRP C  89 
 HIS   0.009   0.002   HIS C   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 ( 7089)
  covalent geometry    : angle       0.73553 ( 9624)
  hydrogen bonds       : bond        0.03502 (   53)
  hydrogen bonds       : angle       5.59622 (  126)

*********************** 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
  102 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.188 
Fit side-chains
REVERT: B  134 ILE cc_start: 0.8607 (mt) cc_final: 0.8302 (tt)
REVERT: A   46 GLU cc_start: 0.6116 (pp20) cc_final: 0.5871 (pp20)
REVERT: A  297 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8239 (mm)
REVERT: C  285 SER cc_start: 0.8485 (t) cc_final: 0.8233 (p)
  outliers start: 29
  outliers final: 15
  residues processed: 96
  average time/residue: 0.0590
  time to fit residues: 8.0820
Evaluate side-chains
  81 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
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   98 VAL
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  226 LEU
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   98 VAL
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 0 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 87 optimal weight:    0.3980
   overall best weight:    2.8788

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.108569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099323 restraints weight = 12787.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.101523 restraints weight = 7182.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.102990 restraints weight = 4693.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.103981 restraints weight = 3401.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104685 restraints weight = 2643.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.5009

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= 0.138
  Angle     :  0.527   9.133   9624  Z= 0.275
  Chirality :  0.045   0.144   1134
  Planarity :  0.004   0.029   1245
  Dihedral  :  4.802  50.851    983
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.97 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.26), residues: 912
  helix:  0.40 (1.06), residues: 30
  sheet: -0.50 (0.25), residues: 405
  loop : -1.47 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  52 
 TYR   0.022   0.001   TYR C  17 
 PHE   0.012   0.002   PHE A 230 
 TRP   0.002   0.001   TRP B  89 
 HIS   0.005   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7089)
  covalent geometry    : angle       0.52722 ( 9624)
  hydrogen bonds       : bond        0.02669 (   53)
  hydrogen bonds       : angle       4.89315 (  126)

*********************** 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
  86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.195 
Fit side-chains
REVERT: B   17 TYR cc_start: 0.8396 (t80) cc_final: 0.8168 (t80)
REVERT: B   75 GLU cc_start: 0.7701 (tp30) cc_final: 0.7440 (tp30)
REVERT: B  134 ILE cc_start: 0.8485 (mt) cc_final: 0.8153 (tt)
REVERT: B  219 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.7871 (ttp80)
REVERT: A  284 LEU cc_start: 0.8090 (tp) cc_final: 0.7872 (tp)
REVERT: A  297 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8040 (mm)
REVERT: C  285 SER cc_start: 0.8389 (t) cc_final: 0.8171 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 84
  average time/residue: 0.0685
  time to fit residues: 8.3158
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  : 0.274 
-------------------------------------------------------------------------------
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  121 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain A residue   57 ILE
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  236 VAL
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 23 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    4.3188

-------------------------------------------------------------------------------
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 = 0.3325 r_free = 0.3325 target = 0.102797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.093809 restraints weight = 13388.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.095867 restraints weight = 7626.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.097249 restraints weight = 5056.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.098201 restraints weight = 3698.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098830 restraints weight = 2894.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   7089  Z= 0.199
  Angle     :  0.593   8.055   9624  Z= 0.308
  Chirality :  0.046   0.132   1134
  Planarity :  0.005   0.034   1245
  Dihedral  :  5.096  46.936    983
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.06 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.25), residues: 912
  helix:  0.25 (1.05), residues: 30
  sheet: -0.83 (0.27), residues: 351
  loop : -1.61 (0.23), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  52 
 TYR   0.018   0.002   TYR A  17 
 PHE   0.019   0.002   PHE B 176 
 TRP   0.002   0.001   TRP B  89 
 HIS   0.008   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 7089)
  covalent geometry    : angle       0.59319 ( 9624)
  hydrogen bonds       : bond        0.02994 (   53)
  hydrogen bonds       : angle       4.87129 (  126)

*********************** 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
  93 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.174 
Fit side-chains
REVERT: B   17 TYR cc_start: 0.8391 (t80) cc_final: 0.8111 (t80)
REVERT: B   75 GLU cc_start: 0.7817 (tp30) cc_final: 0.7558 (tp30)
REVERT: B  134 ILE cc_start: 0.8547 (mt) cc_final: 0.8235 (tt)
REVERT: B  146 ILE cc_start: 0.8869 (pt) cc_final: 0.8658 (pt)
REVERT: A  126 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8362 (mt-10)
REVERT: A  297 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8078 (mm)
REVERT: C  187 ILE cc_start: 0.7458 (mm) cc_final: 0.7254 (mm)
  outliers start: 25
  outliers final: 19
  residues processed: 91
  average time/residue: 0.0511
  time to fit residues: 7.2105
Evaluate side-chains
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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  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  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  113 THR
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   34 THR
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  252 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 89 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0470
   overall best weight:    3.3284

-------------------------------------------------------------------------------
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 = 0.103416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.094407 restraints weight = 13349.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.096507 restraints weight = 7574.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.097899 restraints weight = 4976.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.098861 restraints weight = 3616.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.099528 restraints weight = 2816.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.5471

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= 0.156
  Angle     :  0.538   8.401   9624  Z= 0.280
  Chirality :  0.045   0.152   1134
  Planarity :  0.004   0.031   1245
  Dihedral  :  4.870  43.817    983
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.84 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.25), residues: 912
  helix:  0.38 (1.05), residues: 30
  sheet: -0.83 (0.27), residues: 351
  loop : -1.57 (0.23), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  52 
 TYR   0.022   0.002   TYR A  17 
 PHE   0.013   0.002   PHE B 176 
 TRP   0.002   0.001   TRP B  89 
 HIS   0.007   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7089)
  covalent geometry    : angle       0.53799 ( 9624)
  hydrogen bonds       : bond        0.02773 (   53)
  hydrogen bonds       : angle       4.67139 (  126)

*********************** 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
  90 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.269 
Fit side-chains
REVERT: B   17 TYR cc_start: 0.8426 (t80) cc_final: 0.8130 (t80)
REVERT: B   75 GLU cc_start: 0.7594 (tp30) cc_final: 0.7328 (tp30)
REVERT: B  134 ILE cc_start: 0.8494 (mt) cc_final: 0.8144 (tt)
REVERT: B  146 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8598 (pt)
REVERT: A  297 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8012 (mm)
REVERT: C   17 TYR cc_start: 0.8320 (t80) cc_final: 0.7723 (t80)
REVERT: C  187 ILE cc_start: 0.7464 (mm) cc_final: 0.7257 (mm)
  outliers start: 24
  outliers final: 18
  residues processed: 86
  average time/residue: 0.0484
  time to fit residues: 6.6860
Evaluate side-chains
  81 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  146 ILE
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  113 THR
Chi-restraints excluded: chain A residue  146 ILE
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  150 ASN
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  252 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 55 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 56 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    9.9990
   overall best weight:    4.9586

-------------------------------------------------------------------------------
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 = 0.3271 r_free = 0.3271 target = 0.099795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.090825 restraints weight = 13250.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.092916 restraints weight = 7547.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.094330 restraints weight = 4956.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.095304 restraints weight = 3584.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.095990 restraints weight = 2774.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.5726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   7089  Z= 0.221
  Angle     :  0.611   8.076   9624  Z= 0.318
  Chirality :  0.047   0.137   1134
  Planarity :  0.005   0.036   1245
  Dihedral  :  5.291  50.382    983
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.25), residues: 912
  helix:  0.19 (1.05), residues: 30
  sheet: -0.93 (0.27), residues: 351
  loop : -1.65 (0.23), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  52 
 TYR   0.016   0.002   TYR C  17 
 PHE   0.020   0.002   PHE B 176 
 TRP   0.003   0.001   TRP B  89 
 HIS   0.008   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 7089)
  covalent geometry    : angle       0.61107 ( 9624)
  hydrogen bonds       : bond        0.03133 (   53)
  hydrogen bonds       : angle       4.83590 (  126)

*********************** 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
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 62
  time to evaluate  : 0.283 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7704 (tp30) cc_final: 0.7490 (tp30)
REVERT: B  134 ILE cc_start: 0.8526 (mt) cc_final: 0.8234 (tt)
REVERT: A  268 LYS cc_start: 0.8310 (mttm) cc_final: 0.7931 (mtpt)
REVERT: C   30 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8070 (mtp180)
REVERT: C  157 THR cc_start: 0.8073 (m) cc_final: 0.7753 (p)
  outliers start: 35
  outliers final: 28
  residues processed: 92
  average time/residue: 0.0590
  time to fit residues: 8.1121
Evaluate side-chains
  86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  151 GLN
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  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  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   84 LEU
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  252 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:    0.1980
   chunk 18 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0270
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.2440

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

Flipped N/Q/H residues before XYZ refinement:
B 128 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.105144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.096329 restraints weight = 13353.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.098444 restraints weight = 7428.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.099835 restraints weight = 4821.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100809 restraints weight = 3468.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.101445 restraints weight = 2666.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.5652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7089  Z= 0.087
  Angle     :  0.485   8.861   9624  Z= 0.252
  Chirality :  0.043   0.176   1134
  Planarity :  0.003   0.028   1245
  Dihedral  :  4.593  53.929    983
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.40 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.27), residues: 912
  helix:  0.81 (1.08), residues: 30
  sheet: -0.43 (0.26), residues: 405
  loop : -1.40 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.019   0.001   TYR C  17 
 PHE   0.006   0.001   PHE A 230 
 TRP   0.001   0.000   TRP B  89 
 HIS   0.006   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 7089)
  covalent geometry    : angle       0.48508 ( 9624)
  hydrogen bonds       : bond        0.02417 (   53)
  hydrogen bonds       : angle       4.43599 (  126)

*********************** 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
  71 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.175 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7658 (tp30) cc_final: 0.7408 (tp30)
REVERT: B  134 ILE cc_start: 0.8402 (mt) cc_final: 0.8032 (tt)
REVERT: B  268 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8126 (mtpt)
REVERT: A   46 GLU cc_start: 0.5461 (pp20) cc_final: 0.3606 (pm20)
REVERT: A  130 MET cc_start: 0.8034 (ttp) cc_final: 0.7830 (tmm)
REVERT: C   17 TYR cc_start: 0.8272 (t80) cc_final: 0.7730 (t80)
REVERT: C   30 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8073 (mtp180)
  outliers start: 13
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0595
  time to fit residues: 6.0482
Evaluate side-chains
  68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 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  291 GLU
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   84 LEU
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  193 LEU
Chi-restraints excluded: chain C residue  236 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 29 optimal weight:    0.2980
   chunk 68 optimal weight:    0.0980
   chunk 15 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0270
   overall best weight:    0.6842

-------------------------------------------------------------------------------
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 = 0.3390 r_free = 0.3390 target = 0.107139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.098298 restraints weight = 13220.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.100440 restraints weight = 7338.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.101860 restraints weight = 4734.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.102832 restraints weight = 3388.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.103486 restraints weight = 2599.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7089  Z= 0.076
  Angle     :  0.470   8.652   9624  Z= 0.240
  Chirality :  0.042   0.170   1134
  Planarity :  0.003   0.033   1245
  Dihedral  :  4.160  55.164    983
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 20.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.27), residues: 912
  helix:  1.07 (1.07), residues: 30
  sheet: -0.20 (0.27), residues: 402
  loop : -1.18 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.018   0.001   TYR A 292 
 PHE   0.006   0.001   PHE C  74 
 TRP   0.001   0.000   TRP C  89 
 HIS   0.008   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00167 ( 7089)
  covalent geometry    : angle       0.47043 ( 9624)
  hydrogen bonds       : bond        0.02113 (   53)
  hydrogen bonds       : angle       4.17446 (  126)

*********************** 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
  72 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.249 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7514 (tp30) cc_final: 0.7244 (tp30)
REVERT: B  134 ILE cc_start: 0.8363 (mt) cc_final: 0.8100 (tt)
REVERT: B  268 LYS cc_start: 0.8632 (ptpt) cc_final: 0.8157 (mtpt)
REVERT: A   46 GLU cc_start: 0.5274 (pp20) cc_final: 0.4345 (mm-30)
REVERT: C   17 TYR cc_start: 0.8238 (t80) cc_final: 0.7760 (t80)
REVERT: C  130 MET cc_start: 0.7886 (ttp) cc_final: 0.7516 (tmm)
  outliers start: 11
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0625
  time to fit residues: 6.7244
Evaluate side-chains
  63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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  193 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  252 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 65 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.092793 restraints weight = 13049.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094943 restraints weight = 7397.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.096377 restraints weight = 4833.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.097358 restraints weight = 3476.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098033 restraints weight = 2681.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.5808

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= 0.169
  Angle     :  0.545   7.887   9624  Z= 0.282
  Chirality :  0.045   0.154   1134
  Planarity :  0.004   0.033   1245
  Dihedral  :  4.497  42.136    983
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.40 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.27), residues: 912
  helix:  0.60 (1.05), residues: 30
  sheet: -0.24 (0.27), residues: 405
  loop : -1.36 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 219 
 TYR   0.019   0.002   TYR C  17 
 PHE   0.015   0.002   PHE A 176 
 TRP   0.003   0.001   TRP B  89 
 HIS   0.007   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7089)
  covalent geometry    : angle       0.54535 ( 9624)
  hydrogen bonds       : bond        0.02581 (   53)
  hydrogen bonds       : angle       4.50490 (  126)

********************** 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
  70 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.292 
Fit side-chains
REVERT: B   75 GLU cc_start: 0.7533 (tp30) cc_final: 0.7322 (tp30)
REVERT: B  134 ILE cc_start: 0.8485 (mt) cc_final: 0.8121 (tt)
REVERT: B  268 LYS cc_start: 0.8652 (ptpt) cc_final: 0.8124 (mtpt)
REVERT: A   46 GLU cc_start: 0.5716 (pp20) cc_final: 0.3882 (pm20)
REVERT: A  268 LYS cc_start: 0.8315 (mttm) cc_final: 0.7919 (mtpt)
REVERT: A  273 GLN cc_start: 0.7750 (tt0) cc_final: 0.7529 (tt0)
REVERT: A  275 ASP cc_start: 0.7183 (m-30) cc_final: 0.6929 (m-30)
REVERT: C   17 TYR cc_start: 0.8344 (t80) cc_final: 0.7817 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 69
  average time/residue: 0.0579
  time to fit residues: 6.0808
Evaluate side-chains
  66 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
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  193 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain C residue    9 MET
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  252 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    0.0030
   chunk 9 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0370
   chunk 58 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.9672

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

Flipped N/Q/H residues before XYZ refinement:
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094366 restraints weight = 13294.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.096455 restraints weight = 7602.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.097784 restraints weight = 4995.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098796 restraints weight = 3667.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099448 restraints weight = 2836.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7089  Z= 0.106
  Angle     :  0.500   9.362   9624  Z= 0.255
  Chirality :  0.043   0.176   1134
  Planarity :  0.004   0.032   1245
  Dihedral  :  4.101  26.410    983
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 19.92 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.27), residues: 912
  helix:  0.77 (1.06), residues: 30
  sheet: -0.18 (0.27), residues: 405
  loop : -1.28 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 219 
 TYR   0.018   0.001   TYR C  17 
 PHE   0.009   0.001   PHE C  74 
 TRP   0.002   0.001   TRP C  89 
 HIS   0.006   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7089)
  covalent geometry    : angle       0.50014 ( 9624)
  hydrogen bonds       : bond        0.02324 (   53)
  hydrogen bonds       : angle       4.34007 (  126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 922.62 seconds
wall clock time: 16 minutes 38.27 seconds (998.27 seconds total)