Starting phenix.real_space_refine
on Wed Mar 12 17:33:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jz3_22529/03_2025/7jz3_22529_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jz3_22529/03_2025/7jz3_22529.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2025/7jz3_22529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2025/7jz3_22529.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2025/7jz3_22529_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2025/7jz3_22529_neut.cif"
  }
  resolution = 2.56
  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
-------------------------------------------------------------------------------
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=  -0.000 sd=   0.212
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       9      5.16       5
     C    5097      2.51       5
     N    1374      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8142
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2714
          Classifications: {'peptide': 346}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 342}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 4.66, per 1000 atoms: 0.57
  Number of scatterers: 8142
  At special positions: 0
  Unit cell: (93.96, 92.88, 71.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       9     16.00
     O    1662      8.00
     N    1374      7.00
     C    5097      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: 1.93
  Conformation dependent library (CDL) restraints added in 946.1 milliseconds
  

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1794

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 3 sheets defined
      6.4% alpha, 47.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'B' and resid 97 through 102
    Processing helix  chain 'B' and resid 103 through 105
      No H-bonds generated for 'chain 'B' and resid 103 through 105'
    Processing helix  chain 'B' and resid 171 through 175
      removed outlier: 3.551A  pdb=" N   GLN B 175 " --> pdb=" O   ALA B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 331
    Processing helix  chain 'C' and resid 97 through 102
    Processing helix  chain 'C' and resid 103 through 105
      No H-bonds generated for 'chain 'C' and resid 103 through 105'
    Processing helix  chain 'C' and resid 171 through 175
      removed outlier: 3.551A  pdb=" N   GLN C 175 " --> pdb=" O   ALA C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 324 through 331
    Processing helix  chain 'A' and resid 97 through 102
    Processing helix  chain 'A' and resid 103 through 105
      No H-bonds generated for 'chain 'A' and resid 103 through 105'
    Processing helix  chain 'A' and resid 171 through 175
      removed outlier: 3.551A  pdb=" N   GLN A 175 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 4 through 5
    current: chain 'B' and resid 50 through 61
      removed outlier: 3.584A  pdb=" N   VAL B  75 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   GLN B  59 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   THR B  73 " --> pdb=" O   GLN B  59 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   GLN B  61 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER B  71 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B  91 " --> pdb=" O   PHE B 128 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ASN B  93 " --> pdb=" O   ASN B 126 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ASN B 126 " --> pdb=" O   ASN B  93 " (cutoff:3.500A)
      removed outlier: 11.409A  pdb=" N   ARG B 217 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ALA B 244 " --> pdb=" O   ARG B 217 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   ASN B 254 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   THR B 245 " --> pdb=" O   TRP B 252 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   TRP B 252 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS B 255 " --> pdb=" O   LYS B 283 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LYS B 283 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 257 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN B 279 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR B 265 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   GLY B 282 " --> pdb=" O   ASP B 293 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ASP B 293 " --> pdb=" O   GLY B 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 5
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 4 through 5
    current: chain 'C' and resid 50 through 61
      removed outlier: 3.584A  pdb=" N   VAL C  75 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   GLN C  59 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
      removed outlier: 5.436A  pdb=" N   THR C  73 " --> pdb=" O   GLN C  59 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   GLN C  61 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER C  71 " --> pdb=" O   GLN C  61 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY C  91 " --> pdb=" O   PHE C 128 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ASN C  93 " --> pdb=" O   ASN C 126 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ASN C 126 " --> pdb=" O   ASN C  93 " (cutoff:3.500A)
      removed outlier: 11.409A  pdb=" N   ARG C 217 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   ALA C 244 " --> pdb=" O   ARG C 217 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   ASN C 254 " --> pdb=" O   ASN C 243 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   THR C 245 " --> pdb=" O   TRP C 252 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   TRP C 252 " --> pdb=" O   THR C 245 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS C 255 " --> pdb=" O   LYS C 283 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LYS C 283 " --> pdb=" O   LYS C 255 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 257 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN C 279 " --> pdb=" O   PHE C 259 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR C 265 " --> pdb=" O   PRO C 273 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   GLY C 282 " --> pdb=" O   ASP C 293 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ASP C 293 " --> pdb=" O   GLY C 282 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 5
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 4 through 5
    current: chain 'A' and resid 50 through 61
      removed outlier: 3.584A  pdb=" N   VAL A  75 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   THR A  73 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   GLN A  61 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER A  71 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY A  91 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ASN A  93 " --> pdb=" O   ASN A 126 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ASN A 126 " --> pdb=" O   ASN A  93 " (cutoff:3.500A)
      removed outlier: 11.409A  pdb=" N   ARG A 217 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ALA A 244 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ASN A 254 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   THR A 245 " --> pdb=" O   TRP A 252 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   TRP A 252 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS A 255 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LYS A 283 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 257 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN A 279 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TYR A 265 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   GLY A 282 " --> pdb=" O   ASP A 293 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ASP A 293 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    1089 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: 2.29

  Time building geometry restraints manager: 2.28 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: 2154
        1.33 -     1.45: 1915
        1.45 -     1.57: 4232
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 8319
  Sorted by residual:
  bond pdb=" CA  ASN C 133 "
       pdb=" CB  ASN C 133 "
    ideal  model  delta    sigma   weight residual
    1.530  1.491  0.039 1.55e-02 4.16e+03 6.37e+00
  bond pdb=" CA  ASN B 133 "
       pdb=" CB  ASN B 133 "
    ideal  model  delta    sigma   weight residual
    1.530  1.491  0.039 1.55e-02 4.16e+03 6.26e+00
  bond pdb=" CA  ASN A 133 "
       pdb=" CB  ASN A 133 "
    ideal  model  delta    sigma   weight residual
    1.530  1.492  0.039 1.55e-02 4.16e+03 6.21e+00
  bond pdb=" N   ASN C 133 "
       pdb=" CA  ASN C 133 "
    ideal  model  delta    sigma   weight residual
    1.455  1.427  0.028 1.22e-02 6.72e+03 5.39e+00
  bond pdb=" N   ASN A 133 "
       pdb=" CA  ASN A 133 "
    ideal  model  delta    sigma   weight residual
    1.455  1.428  0.028 1.22e-02 6.72e+03 5.11e+00
  ... (remaining 8314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 10773
        1.39 -     2.79: 428
        2.79 -     4.18: 53
        4.18 -     5.57: 8
        5.57 -     6.97: 3
  Bond angle restraints: 11265
  Sorted by residual:
  angle pdb=" N   VAL B  29 "
        pdb=" CA  VAL B  29 "
        pdb=" C   VAL B  29 "
      ideal   model   delta    sigma   weight residual
     113.53  109.81    3.72 9.80e-01 1.04e+00 1.44e+01
  angle pdb=" N   VAL C  29 "
        pdb=" CA  VAL C  29 "
        pdb=" C   VAL C  29 "
      ideal   model   delta    sigma   weight residual
     113.53  109.83    3.70 9.80e-01 1.04e+00 1.42e+01
  angle pdb=" N   VAL A  29 "
        pdb=" CA  VAL A  29 "
        pdb=" C   VAL A  29 "
      ideal   model   delta    sigma   weight residual
     113.53  109.85    3.68 9.80e-01 1.04e+00 1.41e+01
  angle pdb=" N   GLY C 138 "
        pdb=" CA  GLY C 138 "
        pdb=" C   GLY C 138 "
      ideal   model   delta    sigma   weight residual
     115.32  119.34   -4.02 1.38e+00 5.25e-01 8.49e+00
  angle pdb=" N   GLY B 138 "
        pdb=" CA  GLY B 138 "
        pdb=" C   GLY B 138 "
      ideal   model   delta    sigma   weight residual
     115.32  119.33   -4.01 1.38e+00 5.25e-01 8.43e+00
  ... (remaining 11260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.34: 4233
       16.34 -    32.69: 365
       32.69 -    49.03: 88
       49.03 -    65.37: 15
       65.37 -    81.71: 6
  Dihedral angle restraints: 4707
    sinusoidal: 1791
      harmonic: 2916
  Sorted by residual:
  dihedral pdb=" CA  GLN A 237 "
           pdb=" CB  GLN A 237 "
           pdb=" CG  GLN A 237 "
           pdb=" CD  GLN A 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.89   50.89     3      1.50e+01 4.44e-03 8.95e+00
  dihedral pdb=" CA  GLN B 237 "
           pdb=" CB  GLN B 237 "
           pdb=" CG  GLN B 237 "
           pdb=" CD  GLN B 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.88   50.88     3      1.50e+01 4.44e-03 8.95e+00
  dihedral pdb=" CA  GLN C 237 "
           pdb=" CB  GLN C 237 "
           pdb=" CG  GLN C 237 "
           pdb=" CD  GLN C 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.86   50.86     3      1.50e+01 4.44e-03 8.95e+00
  ... (remaining 4704 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 722
       0.037 -    0.073: 279
       0.073 -    0.110: 91
       0.110 -    0.147: 30
       0.147 -    0.183: 6
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" CA  PHE C 136 "
            pdb=" N   PHE C 136 "
            pdb=" C   PHE C 136 "
            pdb=" CB  PHE C 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" CA  PHE B 136 "
            pdb=" N   PHE B 136 "
            pdb=" C   PHE B 136 "
            pdb=" CB  PHE B 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.90e-01
  chirality pdb=" CA  PHE A 136 "
            pdb=" N   PHE A 136 "
            pdb=" C   PHE A 136 "
            pdb=" CB  PHE A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.90e-01
  ... (remaining 1125 not shown)

  Planarity restraints: 1530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A  84 "   -0.008 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" CG  ASP A  84 "    0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASP A  84 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP A  84 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C  84 "   -0.008 2.00e-02 2.50e+03   1.71e-02 2.94e+00
        pdb=" CG  ASP C  84 "    0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASP C  84 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP C  84 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B  84 "   -0.008 2.00e-02 2.50e+03   1.70e-02 2.91e+00
        pdb=" CG  ASP B  84 "    0.029 2.00e-02 2.50e+03
        pdb=" OD1 ASP B  84 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP B  84 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1527 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 838
        2.75 -     3.29: 7936
        3.29 -     3.82: 13672
        3.82 -     4.36: 17117
        4.36 -     4.90: 30181
  Nonbonded interactions: 69744
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 237 "
            pdb=" OG1 THR B 239 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" NE2 GLN C 237 "
            pdb=" OG1 THR C 239 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" NE2 GLN A 237 "
            pdb=" OG1 THR A 239 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD2 ASP A  89 "
            pdb=" ND2 ASN A  93 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OD2 ASP B  89 "
            pdb=" ND2 ASN B  93 "
     model   vdw
     2.289 3.120
  ... (remaining 69739 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.130
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.670
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:11.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6025
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      :  0.003   0.039   8319  Z= 0.213
  Angle     :  0.623   6.968  11265  Z= 0.384
  Chirality :  0.046   0.183   1128
  Planarity :  0.003   0.038   1530
  Dihedral  : 13.643  81.714   2913
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.27 %
    Favored  : 91.64 %
  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: -2.54 (0.23), residues: 1032
  helix: -2.59 (0.66), residues: 42
  sheet: -0.80 (0.20), residues: 561
  loop : -2.78 (0.24), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  56 
 HIS   0.002   0.001   HIS C  21 
 PHE   0.011   0.002   PHE B 269 
 TYR   0.012   0.001   TYR B  58 
 ARG   0.001   0.000   ARG C 202 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 194
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: B  281 LYS cc_start: 0.5712 (mttm) cc_final: 0.5058 (mptt)
REVERT: B  291 ASP cc_start: 0.5276 (m-30) cc_final: 0.4920 (t0)
REVERT: C  281 LYS cc_start: 0.5715 (mttm) cc_final: 0.5460 (mttm)
REVERT: C  310 MET cc_start: 0.7723 (tpt) cc_final: 0.7399 (tpt)
REVERT: A  281 LYS cc_start: 0.5722 (mttm) cc_final: 0.5054 (mptt)
REVERT: A  291 ASP cc_start: 0.5277 (m-30) cc_final: 0.4989 (t0)
REVERT: A  319 ASN cc_start: 0.5859 (t0) cc_final: 0.5251 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 203
  average time/residue: 0.8646
  time to fit residues: 190.1483
Evaluate side-chains
  156 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain C residue  134 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain A residue  134 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
B   9 ASN
B  21 HIS
B  45 GLN
B  61 GLN
B  83 GLN
B 144 ASN
B 231 ASN
B 237 GLN
B 264 GLN
C  21 HIS
C  45 GLN
C  61 GLN
C 144 ASN
** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
A   9 ASN
A  21 HIS
A  45 GLN
A  61 GLN
A 144 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 231 ASN
A 264 GLN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.249873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.238342 restraints weight = 9726.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.4727 rms_B_bonded: 1.78
r_work: 0.4680 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4589 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.4589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6467
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053   8319  Z= 0.488
  Angle     :  0.910  12.523  11265  Z= 0.487
  Chirality :  0.054   0.159   1128
  Planarity :  0.006   0.049   1530
  Dihedral  :  6.307  54.933   1171
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 17.82 %
    Favored  : 75.88 %
  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: -2.76 (0.23), residues: 1032
  helix: -2.66 (0.50), residues: 60
  sheet: -0.72 (0.20), residues: 543
  loop : -3.21 (0.23), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 252 
 HIS   0.002   0.001   HIS A  21 
 PHE   0.039   0.004   PHE C  40 
 TYR   0.026   0.003   TYR C 313 
 ARG   0.010   0.002   ARG A 170 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 177
  time to evaluate  : 0.838 
Fit side-chains
REVERT: B   23 PHE cc_start: 0.4298 (m-80) cc_final: 0.3476 (m-80)
REVERT: B  178 ASP cc_start: 0.6828 (m-30) cc_final: 0.6546 (m-30)
REVERT: B  189 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6857 (tm-30)
REVERT: B  212 ILE cc_start: 0.7114 (pt) cc_final: 0.6845 (pt)
REVERT: B  237 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5759 (tt0)
REVERT: B  252 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.5646 (m-90)
REVERT: B  281 LYS cc_start: 0.5319 (mttm) cc_final: 0.4154 (mttt)
REVERT: C   27 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6902 (mmtp)
REVERT: C   83 GLN cc_start: 0.7990 (pt0) cc_final: 0.7746 (pt0)
REVERT: C  189 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6832 (tm-30)
REVERT: C  217 ARG cc_start: 0.6084 (mtp85) cc_final: 0.5712 (mtp85)
REVERT: C  219 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.3925 (mp0)
REVERT: C  281 LYS cc_start: 0.5449 (mttm) cc_final: 0.4472 (mttt)
REVERT: C  310 MET cc_start: 0.7906 (tpt) cc_final: 0.7598 (tpt)
REVERT: A   50 LEU cc_start: 0.7638 (tm) cc_final: 0.7416 (tm)
REVERT: A   73 THR cc_start: 0.7708 (p) cc_final: 0.7484 (t)
REVERT: A  121 MET cc_start: 0.6987 (mmm) cc_final: 0.6643 (mmm)
REVERT: A  189 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6795 (tm-30)
REVERT: A  281 LYS cc_start: 0.5610 (mttm) cc_final: 0.4453 (mptt)
REVERT: A  287 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7205 (mtp85)
  outliers start: 52
  outliers final: 21
  residues processed: 207
  average time/residue: 0.8736
  time to fit residues: 195.2796
Evaluate side-chains
  196 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  252 TRP
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  308 LYS
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  219 GLU
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  304 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0070
   chunk 15 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.9804

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 ASN
B 148 GLN
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   9 ASN
C 144 ASN
** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
A 148 GLN
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4949 r_free = 0.4949 target = 0.262368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.250715 restraints weight = 9691.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.4819 rms_B_bonded: 1.84
r_work: 0.4776 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.4688 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.4688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6248
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8319  Z= 0.170
  Angle     :  0.640   9.037  11265  Z= 0.340
  Chirality :  0.046   0.140   1128
  Planarity :  0.004   0.050   1530
  Dihedral  :  4.997  39.836   1170
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 24.36 %
    Favored  : 72.24 %
  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: -2.19 (0.24), residues: 1032
  helix: -1.96 (0.61), residues: 60
  sheet: -0.51 (0.21), residues: 558
  loop : -2.67 (0.25), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  56 
 HIS   0.001   0.000   HIS A  21 
 PHE   0.022   0.001   PHE C  40 
 TYR   0.020   0.002   TYR A  98 
 ARG   0.006   0.001   ARG B 174 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.847 
Fit side-chains
REVERT: B  178 ASP cc_start: 0.6973 (m-30) cc_final: 0.6745 (m-30)
REVERT: B  281 LYS cc_start: 0.5207 (mttm) cc_final: 0.4291 (mttp)
REVERT: B  319 ASN cc_start: 0.6624 (t0) cc_final: 0.6276 (t0)
REVERT: C   27 LYS cc_start: 0.7377 (mptt) cc_final: 0.6652 (mmtp)
REVERT: C   92 ARG cc_start: 0.5797 (ttt180) cc_final: 0.5556 (tpt170)
REVERT: C  189 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6764 (tm-30)
REVERT: C  255 LYS cc_start: 0.6160 (mttt) cc_final: 0.5909 (mttp)
REVERT: C  281 LYS cc_start: 0.5222 (mttm) cc_final: 0.4185 (mttp)
REVERT: A   12 ASP cc_start: 0.5931 (p0) cc_final: 0.5628 (p0)
REVERT: A  189 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6596 (tm-30)
REVERT: A  255 LYS cc_start: 0.6082 (mttt) cc_final: 0.5760 (mttp)
REVERT: A  274 SER cc_start: 0.7821 (p) cc_final: 0.7592 (t)
REVERT: A  281 LYS cc_start: 0.5600 (mttm) cc_final: 0.4386 (mptt)
REVERT: A  291 ASP cc_start: 0.6397 (m-30) cc_final: 0.6148 (t0)
  outliers start: 28
  outliers final: 16
  residues processed: 193
  average time/residue: 0.8725
  time to fit residues: 182.2656
Evaluate side-chains
  175 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  268 ASP
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue  289 TYR
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  289 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 91 optimal weight:    8.9990
   chunk 70 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 84 optimal weight:   20.0000
   chunk 92 optimal weight:    0.0030
   chunk 62 optimal weight:   10.0000
   overall best weight:    4.5998

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 150 GLN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.253847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.242363 restraints weight = 9677.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.4752 rms_B_bonded: 1.80
r_work: 0.4711 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4623 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.4623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8319  Z= 0.329
  Angle     :  0.752   9.540  11265  Z= 0.404
  Chirality :  0.049   0.169   1128
  Planarity :  0.005   0.056   1530
  Dihedral  :  5.283  18.915   1164
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 25.09 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.24), residues: 1032
  helix: -2.28 (0.59), residues: 60
  sheet: -0.50 (0.21), residues: 552
  loop : -2.87 (0.24), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 252 
 HIS   0.002   0.001   HIS A  21 
 PHE   0.021   0.003   PHE C  40 
 TYR   0.022   0.002   TYR A 227 
 ARG   0.006   0.001   ARG B 170 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 170
  time to evaluate  : 0.844 
Fit side-chains
REVERT: B   57 GLU cc_start: 0.7774 (tt0) cc_final: 0.7421 (tt0)
REVERT: B  120 PHE cc_start: 0.6128 (m-80) cc_final: 0.5915 (m-80)
REVERT: B  178 ASP cc_start: 0.6919 (m-30) cc_final: 0.6668 (m-30)
REVERT: B  189 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7020 (tm-30)
REVERT: B  252 TRP cc_start: 0.6796 (OUTLIER) cc_final: 0.5412 (m-90)
REVERT: B  281 LYS cc_start: 0.5350 (mttm) cc_final: 0.4245 (mttt)
REVERT: B  319 ASN cc_start: 0.7043 (t0) cc_final: 0.6726 (t0)
REVERT: C   27 LYS cc_start: 0.7447 (mptt) cc_final: 0.6731 (mmtp)
REVERT: C  126 ASN cc_start: 0.7268 (m110) cc_final: 0.6991 (m-40)
REVERT: C  170 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.5473 (ptp-170)
REVERT: C  189 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6808 (tm-30)
REVERT: C  255 LYS cc_start: 0.5971 (mttt) cc_final: 0.5699 (mttp)
REVERT: C  258 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.7039 (m110)
REVERT: C  274 SER cc_start: 0.7751 (p) cc_final: 0.7473 (p)
REVERT: C  281 LYS cc_start: 0.5491 (mttm) cc_final: 0.4446 (mttt)
REVERT: A  255 LYS cc_start: 0.6075 (mttt) cc_final: 0.5706 (mttp)
REVERT: A  281 LYS cc_start: 0.5691 (mttm) cc_final: 0.4502 (mptt)
  outliers start: 49
  outliers final: 27
  residues processed: 202
  average time/residue: 0.9890
  time to fit residues: 215.8064
Evaluate side-chains
  190 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 160
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  252 TRP
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  289 TYR
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  304 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 95 optimal weight:    0.7980
   chunk 6 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
B 126 ASN
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.252155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.240716 restraints weight = 9595.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4737 rms_B_bonded: 1.76
r_work: 0.4695 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4607 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.4607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6422
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   8319  Z= 0.360
  Angle     :  0.779   9.881  11265  Z= 0.419
  Chirality :  0.050   0.183   1128
  Planarity :  0.005   0.058   1530
  Dihedral  :  5.491  20.356   1164
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  7.39 %
    Allowed  : 24.97 %
    Favored  : 67.64 %
  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: -2.42 (0.24), residues: 1032
  helix: -2.46 (0.59), residues: 60
  sheet: -0.46 (0.21), residues: 543
  loop : -3.03 (0.23), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 252 
 HIS   0.002   0.001   HIS A  21 
 PHE   0.020   0.003   PHE C  40 
 TYR   0.025   0.003   TYR A 227 
 ARG   0.006   0.001   ARG A 170 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 168
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: B  178 ASP cc_start: 0.6880 (m-30) cc_final: 0.6658 (m-30)
REVERT: B  189 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6976 (tm-30)
REVERT: B  281 LYS cc_start: 0.5309 (mttm) cc_final: 0.4236 (mttt)
REVERT: C   27 LYS cc_start: 0.7426 (mptt) cc_final: 0.6711 (mmtp)
REVERT: C   73 THR cc_start: 0.7635 (t) cc_final: 0.7301 (m)
REVERT: C   83 GLN cc_start: 0.7575 (pt0) cc_final: 0.7224 (pt0)
REVERT: C  126 ASN cc_start: 0.7196 (m110) cc_final: 0.6963 (m-40)
REVERT: C  170 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.5455 (ptp-170)
REVERT: C  189 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6833 (tm-30)
REVERT: C  258 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.7061 (m110)
REVERT: C  274 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7481 (p)
REVERT: C  281 LYS cc_start: 0.5535 (mttm) cc_final: 0.4509 (mttt)
REVERT: A  170 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5651 (ptp-170)
REVERT: A  189 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6609 (tm-30)
REVERT: A  252 TRP cc_start: 0.6846 (OUTLIER) cc_final: 0.5104 (m-90)
REVERT: A  255 LYS cc_start: 0.6125 (mttt) cc_final: 0.5736 (mttp)
REVERT: A  281 LYS cc_start: 0.5749 (mttm) cc_final: 0.4735 (mttp)
  outliers start: 61
  outliers final: 32
  residues processed: 207
  average time/residue: 0.8667
  time to fit residues: 193.5261
Evaluate side-chains
  192 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  126 ASN
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  252 TRP
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  298 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 264 GLN
** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 GLN
A 144 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.257263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.245473 restraints weight = 9625.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4776 rms_B_bonded: 1.83
r_work: 0.4731 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.4643 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.4643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8319  Z= 0.209
  Angle     :  0.672   9.296  11265  Z= 0.358
  Chirality :  0.046   0.141   1128
  Planarity :  0.004   0.057   1530
  Dihedral  :  4.970  17.941   1164
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 27.64 %
    Favored  : 66.06 %
  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: -2.00 (0.24), residues: 1032
  helix: -1.77 (0.75), residues: 42
  sheet: -0.38 (0.21), residues: 549
  loop : -2.53 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  56 
 HIS   0.002   0.001   HIS A  21 
 PHE   0.016   0.002   PHE C  40 
 TYR   0.022   0.002   TYR A  98 
 ARG   0.004   0.000   ARG B 124 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 167
  time to evaluate  : 0.995 
Fit side-chains
REVERT: B  189 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6926 (tm-30)
REVERT: B  281 LYS cc_start: 0.5138 (mttm) cc_final: 0.4077 (mttt)
REVERT: B  319 ASN cc_start: 0.7003 (t0) cc_final: 0.6699 (t0)
REVERT: C   27 LYS cc_start: 0.7413 (mptt) cc_final: 0.6714 (mmtp)
REVERT: C   73 THR cc_start: 0.7331 (t) cc_final: 0.6972 (m)
REVERT: C   83 GLN cc_start: 0.7606 (pt0) cc_final: 0.7253 (pt0)
REVERT: C  126 ASN cc_start: 0.7253 (m110) cc_final: 0.6986 (m-40)
REVERT: C  170 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.5383 (ptp-170)
REVERT: C  189 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: C  281 LYS cc_start: 0.5583 (mttm) cc_final: 0.4579 (mtmm)
REVERT: C  294 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6821 (mm)
REVERT: C  345 GLN cc_start: 0.7442 (pt0) cc_final: 0.7126 (pt0)
REVERT: A   12 ASP cc_start: 0.6065 (p0) cc_final: 0.5723 (p0)
REVERT: A   96 VAL cc_start: 0.6421 (OUTLIER) cc_final: 0.6079 (m)
REVERT: A  189 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6561 (tm-30)
REVERT: A  255 LYS cc_start: 0.6112 (mttt) cc_final: 0.5717 (mttp)
REVERT: A  281 LYS cc_start: 0.5584 (mttm) cc_final: 0.4379 (mptt)
  outliers start: 52
  outliers final: 34
  residues processed: 203
  average time/residue: 1.1341
  time to fit residues: 247.7877
Evaluate side-chains
  198 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 161
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  289 TYR
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  343 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 101 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0570
   chunk 45 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    5.0106

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

Flipped N/Q/H residues before XYZ refinement:
B 126 ASN
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.252686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.241344 restraints weight = 9695.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.4740 rms_B_bonded: 1.77
r_work: 0.4699 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4611 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.4611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8319  Z= 0.352
  Angle     :  0.793   9.850  11265  Z= 0.424
  Chirality :  0.050   0.176   1128
  Planarity :  0.005   0.058   1530
  Dihedral  :  5.451  20.241   1164
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 28.36 %
    Favored  : 64.36 %
  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: -2.15 (0.24), residues: 1032
  helix: -1.67 (0.79), residues: 42
  sheet: -0.38 (0.22), residues: 543
  loop : -2.77 (0.24), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 252 
 HIS   0.003   0.001   HIS A  21 
 PHE   0.019   0.003   PHE B 120 
 TYR   0.027   0.003   TYR A 227 
 ARG   0.005   0.001   ARG A 170 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 158
  time to evaluate  : 0.794 
Fit side-chains
REVERT: B  189 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: B  252 TRP cc_start: 0.6798 (OUTLIER) cc_final: 0.5321 (m-90)
REVERT: B  281 LYS cc_start: 0.5313 (mttm) cc_final: 0.4188 (mptt)
REVERT: C   27 LYS cc_start: 0.7413 (mptt) cc_final: 0.6710 (mmtp)
REVERT: C   73 THR cc_start: 0.7581 (t) cc_final: 0.7231 (m)
REVERT: C   83 GLN cc_start: 0.7719 (pt0) cc_final: 0.7298 (pt0)
REVERT: C  126 ASN cc_start: 0.7220 (m110) cc_final: 0.6948 (m-40)
REVERT: C  170 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5419 (ptp-170)
REVERT: C  189 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6769 (tm-30)
REVERT: C  274 SER cc_start: 0.7774 (OUTLIER) cc_final: 0.7487 (p)
REVERT: C  281 LYS cc_start: 0.5553 (mttm) cc_final: 0.4666 (mtmm)
REVERT: C  294 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6583 (mm)
REVERT: A   12 ASP cc_start: 0.6130 (p0) cc_final: 0.5798 (p0)
REVERT: A  170 ARG cc_start: 0.5722 (OUTLIER) cc_final: 0.5464 (ptp-170)
REVERT: A  189 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6672 (tm-30)
REVERT: A  252 TRP cc_start: 0.6854 (OUTLIER) cc_final: 0.5125 (m-90)
  outliers start: 60
  outliers final: 41
  residues processed: 195
  average time/residue: 0.8568
  time to fit residues: 181.3702
Evaluate side-chains
  199 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 152
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  252 TRP
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  252 TRP
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  343 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.254558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.243181 restraints weight = 9718.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.4759 rms_B_bonded: 1.78
r_work: 0.4717 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.4629 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.4629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8319  Z= 0.277
  Angle     :  0.742   9.574  11265  Z= 0.395
  Chirality :  0.048   0.164   1128
  Planarity :  0.004   0.058   1530
  Dihedral  :  5.269  19.787   1164
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 29.58 %
    Favored  : 63.76 %
  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: -2.07 (0.24), residues: 1032
  helix: -1.72 (0.76), residues: 42
  sheet: -0.29 (0.22), residues: 540
  loop : -2.76 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 252 
 HIS   0.002   0.001   HIS A  21 
 PHE   0.017   0.002   PHE C  40 
 TYR   0.026   0.002   TYR A  98 
 ARG   0.005   0.001   ARG A 170 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 160
  time to evaluate  : 0.877 
Fit side-chains
REVERT: B   57 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6445 (tp30)
REVERT: B  189 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6880 (tm-30)
REVERT: B  281 LYS cc_start: 0.5269 (mttm) cc_final: 0.4147 (mptt)
REVERT: C   27 LYS cc_start: 0.7435 (mptt) cc_final: 0.6732 (mmtp)
REVERT: C   73 THR cc_start: 0.7418 (t) cc_final: 0.7057 (m)
REVERT: C  120 PHE cc_start: 0.6459 (m-80) cc_final: 0.6027 (m-80)
REVERT: C  126 ASN cc_start: 0.7225 (m110) cc_final: 0.6949 (m-40)
REVERT: C  170 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.5393 (ptp-170)
REVERT: C  189 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6692 (tm-30)
REVERT: C  219 GLU cc_start: 0.4861 (OUTLIER) cc_final: 0.3901 (mp0)
REVERT: C  274 SER cc_start: 0.7700 (p) cc_final: 0.7443 (p)
REVERT: C  281 LYS cc_start: 0.5577 (mttm) cc_final: 0.4677 (mtmm)
REVERT: C  294 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6613 (mm)
REVERT: A   12 ASP cc_start: 0.6081 (p0) cc_final: 0.5741 (p0)
REVERT: A  189 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6653 (tm-30)
REVERT: A  252 TRP cc_start: 0.6782 (OUTLIER) cc_final: 0.5083 (m-90)
REVERT: A  255 LYS cc_start: 0.5911 (mttt) cc_final: 0.5597 (mttp)
  outliers start: 55
  outliers final: 42
  residues processed: 195
  average time/residue: 0.8076
  time to fit residues: 171.2244
Evaluate side-chains
  199 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 152
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  219 GLU
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  289 TYR
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  252 TRP
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  343 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 92 optimal weight:   10.0000
   chunk 24 optimal weight:    0.2980
   chunk 6 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 GLN ** 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 = 0.4891 r_free = 0.4891 target = 0.255429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.244160 restraints weight = 9806.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.4767 rms_B_bonded: 1.77
r_work: 0.4725 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4638 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.4638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8319  Z= 0.257
  Angle     :  0.731   9.488  11265  Z= 0.388
  Chirality :  0.048   0.170   1128
  Planarity :  0.004   0.058   1530
  Dihedral  :  5.184  19.845   1164
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 29.45 %
    Favored  : 63.76 %
  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: -2.09 (0.24), residues: 1032
  helix: -2.17 (0.60), residues: 60
  sheet: -0.31 (0.22), residues: 546
  loop : -2.74 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 252 
 HIS   0.002   0.001   HIS A  21 
 PHE   0.016   0.002   PHE C  40 
 TYR   0.026   0.002   TYR A  98 
 ARG   0.003   0.000   ARG C 170 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 156
  time to evaluate  : 0.840 
Fit side-chains
REVERT: B   57 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6454 (tp30)
REVERT: B  189 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6849 (tm-30)
REVERT: B  281 LYS cc_start: 0.5250 (mttm) cc_final: 0.4150 (mptt)
REVERT: C   27 LYS cc_start: 0.7410 (mptt) cc_final: 0.6715 (mmtp)
REVERT: C   83 GLN cc_start: 0.7409 (pt0) cc_final: 0.7046 (pt0)
REVERT: C  120 PHE cc_start: 0.6237 (m-80) cc_final: 0.5879 (m-80)
REVERT: C  126 ASN cc_start: 0.7229 (m110) cc_final: 0.6962 (m-40)
REVERT: C  170 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5354 (ptp-170)
REVERT: C  189 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6699 (tm-30)
REVERT: C  219 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.3878 (mp0)
REVERT: C  274 SER cc_start: 0.7685 (p) cc_final: 0.7436 (p)
REVERT: C  281 LYS cc_start: 0.5593 (mttm) cc_final: 0.4584 (mtmm)
REVERT: C  345 GLN cc_start: 0.7484 (pt0) cc_final: 0.7164 (pm20)
REVERT: A   12 ASP cc_start: 0.6026 (p0) cc_final: 0.5691 (p0)
REVERT: A  189 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6588 (tm-30)
REVERT: A  252 TRP cc_start: 0.6754 (OUTLIER) cc_final: 0.5072 (m-90)
REVERT: A  255 LYS cc_start: 0.5976 (mttt) cc_final: 0.5614 (mttp)
  outliers start: 56
  outliers final: 42
  residues processed: 193
  average time/residue: 0.8355
  time to fit residues: 174.9816
Evaluate side-chains
  197 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 151
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  219 GLU
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  252 TRP
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  343 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 45 optimal weight:    0.3980
   chunk 86 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
B  69 ASN
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 GLN
C  69 ASN
C 237 GLN
A 144 ASN
A 167 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4927 r_free = 0.4927 target = 0.259401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.247900 restraints weight = 9566.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.4803 rms_B_bonded: 1.79
r_work: 0.4761 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4675 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.4675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6295
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8319  Z= 0.194
  Angle     :  0.679   9.218  11265  Z= 0.361
  Chirality :  0.046   0.131   1128
  Planarity :  0.004   0.058   1530
  Dihedral  :  4.885  17.816   1164
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 31.88 %
    Favored  : 63.39 %
  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: -1.94 (0.24), residues: 1032
  helix: -2.09 (0.60), residues: 60
  sheet: -0.24 (0.21), residues: 549
  loop : -2.59 (0.25), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  56 
 HIS   0.002   0.001   HIS A  21 
 PHE   0.015   0.002   PHE C  40 
 TYR   0.024   0.002   TYR B  98 
 ARG   0.003   0.000   ARG B 287 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 0.774 
Fit side-chains
REVERT: B  189 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: B  252 TRP cc_start: 0.6559 (OUTLIER) cc_final: 0.5079 (m-90)
REVERT: B  281 LYS cc_start: 0.5251 (mttm) cc_final: 0.4008 (mptt)
REVERT: C   27 LYS cc_start: 0.7349 (mptt) cc_final: 0.7139 (mptt)
REVERT: C   83 GLN cc_start: 0.7388 (pt0) cc_final: 0.7060 (pt0)
REVERT: C  126 ASN cc_start: 0.7197 (m110) cc_final: 0.6971 (m-40)
REVERT: C  189 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6694 (tm-30)
REVERT: C  219 GLU cc_start: 0.4867 (OUTLIER) cc_final: 0.3928 (mp0)
REVERT: C  237 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.5826 (tt0)
REVERT: C  281 LYS cc_start: 0.5505 (mttm) cc_final: 0.4345 (mptt)
REVERT: C  345 GLN cc_start: 0.7405 (pt0) cc_final: 0.7049 (pm20)
REVERT: A   12 ASP cc_start: 0.5953 (p0) cc_final: 0.5645 (p0)
REVERT: A  189 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6546 (tm-30)
  outliers start: 39
  outliers final: 33
  residues processed: 185
  average time/residue: 0.8340
  time to fit residues: 167.7913
Evaluate side-chains
  185 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  252 TRP
Chi-restraints excluded: chain B residue  258 ASN
Chi-restraints excluded: chain B residue  268 ASP
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  219 GLU
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  237 GLN
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  289 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  343 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 72 optimal weight:    5.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 237 GLN
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.258286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.246693 restraints weight = 9742.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.4793 rms_B_bonded: 1.80
r_work: 0.4751 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4663 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.4663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6307
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.131   8319  Z= 0.378
  Angle     :  1.455  59.200  11265  Z= 0.818
  Chirality :  0.054   0.718   1128
  Planarity :  0.005   0.056   1530
  Dihedral  :  5.093  34.856   1164
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 31.88 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.99 (0.24), residues: 1032
  helix: -2.10 (0.60), residues: 60
  sheet: -0.28 (0.21), residues: 549
  loop : -2.63 (0.25), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  56 
 HIS   0.003   0.001   HIS A  21 
 PHE   0.016   0.002   PHE C  40 
 TYR   0.022   0.002   TYR B  98 
 ARG   0.003   0.001   ARG C 170 

===============================================================================
Job complete
usr+sys time: 5922.32 seconds
wall clock time: 104 minutes 49.20 seconds (6289.20 seconds total)